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Bioconductor 2.13 Released

October 15, 2013

Bioconductors:

We are pleased to announce Bioconductor 2.13, consisting of 749 software packages, 179 experiment data packages, and more than 690 up-to-date annotation packages.

There are 84 new software packages, and many updates and improvements to existing packages; Bioconductor 2.13 is compatible with R 3.0.2, and is supported on Linux, 32- and 64-bit Windows, and Mac OS X. This release includes an updated Bioconductor Amazon Machine Image.

Visit http://bioconductor.org for details and downloads.

Getting Started with Bioconductor 2.13
New Software Packages
NEWS from new and existing packages
Packages removed from the release

Getting Started with Bioconductor 2.13

To update to or install Bioconductor 2.13:

Install R 3.0.2. Bioconductor 2.13 has been designed expressly for this version of R.
Follow the instructions at http://bioconductor.org/install/

New Software Packages

There are 84 new packages in this release of Bioconductor.

AllelicImbalance: Provides a framework for allelic specific expression investigation using RNA-seq data

ampliQueso: The package provides tools and reports for the analysis of amplicon sequencing panels, such as AmpliSeq

ArrayTV: Wave correction for genotyping and copy number arrays

ASSET: An R package for subset-based analysis of heterogeneous traits and subtypes

BADER: For RNA sequencing count data, BADER fits a Bayesian hierarchical model. The algorithm returns the posterior probability of differential expression for each gene between two groups A and B. The joint posterior distribution of the variables in the model can be returned in the form of posterior samples, which can be used for further down-stream analyses such as gene set enrichment.

BAGS: R package providing functions to perform geneset significance analysis over simple cross-sectional data between 2 and 5 phenotypes of interest.

BiGGR: This package provides an interface to simulate metabolic reconstruction from the BiGG database(http://bigg.ucsd.edu/) and other metabolic reconstruction databases. The package aids in performing flux balance analysis (FBA). Metabolic networks and estimated fluxes can be visualized using hypergraphs.

bioassayR: bioassayR provides tools for statistical analysis of small molecule bioactivity data

BiocParallel: This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.

BiocStyle: Provides standard formatting styles for Bioconductor documents. The vignette illustrates use and functionality.

BiRewire: Fast functions for bipartite network rewiring through N consecutive switching steps (See References) and for the computation of the minimal number of switching steps to be performed in order to maximise the dissimilarity with respect to the original network. Includes function for the analysis of the introduced randomness across the switching and several other routines to analyse the resulting networks and their natural projections. Extension to undirected networks (not bipartite) is also provided.

CexoR: Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function (package ‘skellam’) is used to detect significant normalized count differences of opposed sign at each DNA strand (peak-pairs). Irreproducible discovery rate for overlapping peak-pairs across biological replicates is estimated using the package ‘idr’.

ChAMP: The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number aberrations.

ChemmineOB: ChemmineOB provides an R interface to a subset of cheminformatics functionalities implemented by the OpelBabel C++ project. OpenBabel is an open source cheminformatics toolbox that includes utilities for structure format interconversions, descriptor calculations, compound similarity searching and mor. ChemineOB aims to make a subset of these utilities available from within R. For non-developers, ChemineOB is primarily intended to be used from ChemmineR as an add-on package rather than used directly.

chipenrich: ChIP-Enrich performs gene set enrichment testing using peaks called from a ChIP-seq experiment. The method empirically corrects for confounding factors such as the length of genes, and the mappability of the sequence surrounding genes.

cleanUpdTSeq: This package uses the Naive Bayes classifier (from e1071) to assign probability values to putative polyadenylation sites (pA sites) based on training data from zebrafish. This will allow the user to separate true, biologically relevant pA sites from false, oligodT primed pA sites.

cleaver: In-silico cleavage of polypeptide sequences. The cleavage rules are taken from: http://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html

clonotypeR: High throughput analysis of T cell antigen receptor sequences The genes encoding T cell receptors are created by somatic recombination, generating an immense combination of V, (D) and J segments. Additional processes during the recombination create extra sequence diversity between the V an J segments. Collectively, this hyper-variable region is called the CDR3 loop.

The purpose of this package is to process and quantitatively analyse millions of V-CDR3-J combination, called clonotypes, from multiple sequence libraries.

CNVrd2: CNVrd2 uses next-generation sequencing data to measure human gene copy number for multiple samples, identify SNPs tagging copy number variants and detect copy number polymorphic genomic regions.

cobindR: Finding and analysing co-occuring motifs of transcription factor binding sites in groups of genes

CSSP: Power computation for ChIP-Seq data based on Bayesian estimation for local poisson counting process.

customProDB: Generate customized protein sequence database from RNA-Seq data for proteomics search

dagLogo: Visualize significant conserved amino acid sequence pattern in groups based on probability theory

DNaseR: Strand-specific digital genomic footprinting in DNase-seq data. The cumulative Skellam distribution function (package ‘skellam’) is used to detect significant normalized count differences of opposed sign at each DNA strand. This is done in order to determine the protein-binding footprint flanks. Preprocessing of the mapped reads is recommended before running DNaseR (e.g., quality checking and removal of sequence-specific bias).

EBSeq: Differential Expression analysis at both gene and isoform level using RNA-seq data

epivizr: This package provides Websocket communication to the epiviz web app (http://epiviz.cbcb.umd.edu) for interactive visualization of genomic data. Objects in R/bioc interactive sessions can be displayed in genome browser tracks or plots to be explored by navigation through genomic regions. Fundamental Bioconductor data structures are supported (e.g., GenomicRanges and SummarizedExperiment objects), while providing an easy mechanism to support other data structures. Visualizations (using d3.js) can be easily added to the web app as well.

exomePeak: The package is developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built on the basis of the exomePeak MATLAB package (Meng, Jia, et al. “Exome-based analysis for RNA epigenome sequencing data.” Bioinformatics 29.12 (2013): 1565-1567.) with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome. The exomePeak R-package accepts and statistically supports multiple biological replicates, internally removes PCR artifacts and multi-mapping reads, outputs exome-based binding sites (RNA methylation sites) and detects differential post-transcriptional RNA modification sites between two experimental conditions in term of percentage rather the absolute amount. The package is still under active development, and we welcome all biology and computation scientist for all kinds of collaborations and communications. Please feel free to contact Dr. Jia Meng jia.meng@hotmail.com if you have any questions.

FGNet: Build and visualize functional gene networks from clustering of enrichment analyses in multiple annotation spaces. The package includes an interface to perform the analysis through David and GeneTerm Linker.

flipflop: Flipflop discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data.

flowBeads: This package extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalisation.

flowFit: This package estimate the proliferation of a cell population in cell-tracking dye studies. The package uses an R implementation of the Levenberg-Marquardt algorithm (minpack.lm) to fit a set of peaks (corresponding to different generations of cells) over the proliferation-tracking dye distribution in a FACS experiment.

flowMap: This package provides an algorithm to compare and match cell populations across multiple flow cytometry samples. The method is based on the Friedman-Rafsky test, a nonparametric multivariate statistical test, where two cell distributions match if they occupy a similar feature space. The algorithm allows the users to specify a reference sample for comparison or to construct a reference sample from the available data. The output of the algorithm is a set of text files where the cell population labels are replaced by a metaset of population labels, generated from the matching process.

GOSim: This package implements several functions useful for computing similarities between GO terms and gene products based on their GO annotation. Moreover it allows for computing a GO enrichment analysis

h5vc: This package contains functions to interact with tally data from NGS experiments that is stored in HDF5 files. For detail see the webpage at http://www.ebi.ac.uk/~pyl/h5vc.

intansv: This package provides efficient tools to read and integrate structural variations predicted by popular softwares. Annotation and visulation of structural variations are also implemented in the package.

interactiveDisplay: The interactiveDisplay package contains the methods needed to generate interactive Shiny based display methods for Bioconductor objects.

maPredictDSC: This package implements the classification pipeline of the best overall team (Team221) in the IMPROVER Diagnostic Signature Challenge. Additional functionality is added to compare 27 combinations of data preprocessing, feature selection and classifier types.

metaSeq: The probabilities by one-sided NOISeq are combined by Fisher’s method or Stouffer’s method

methylMnM: To give the exactly p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparation.

mitoODE: The package contains the methods to fit a cell-cycle model on cell count data and the code to reproduce the results shown in the paper “Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay” (submitted).

msmsEDA: Exploratory data analysis to assess the quality of a set of LC-MS/MS experiments, and visualize de influence of the involved factors.

msmsTests: Statistical tests for label-free LC-MS/MS data by spectral counts, to discover differentially expressed proteins between two biological conditions. Three tests are available: Poisson GLM regression, quasi-likelihood GLM regression, and the negative binomial of the edgeR package.The three models admit blocking factors to control for nuissance variables.To assure a good level of reproducibility a post-test filter is available, where we may set the minimum effect size considered biologicaly relevant, and the minimum expression of the most abundant condition.

MSstats: A set of tools for protein significance analysis in label-free or LC-MS, SRM and DIA experiments.

mzID: A parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less ‘pretty’ output than a vendor specific parser. Please contact the maintainer with any problems and supply an mzIdentML file so the problems can be fixed quick.

neaGUI: neaGUI is an easy to use R package developed to perform the network enrichment analysis (NEA) proposed by Alexeyenko et al. (2012). The NEA method extends the overlap statistics in GSEA to network links between genes in the experimental set and those in the functional categories by exploiting biological information in terms of gene interaction network. The neaGUI requires the following R packages: tcltk, KEGG.db, GO.db, reactome.db, org.Hs.eg.db, AnnotationDbi, and hwriter.

NetSAM: The NetSAM (Network Seriation and Modularization) package takes an edge-list representation of a network as an input, performs network seriation and modularization analysis, and generates as files that can be used as an input for the one-dimensional network visualization tool NetGestalt (http://www.netgestalt.org) or other network analysis.

omicade4: Multiple co-inertia analysis of omics datasets

OmicCircos: OmicCircos is an R application and package for generating high-quality circular maps for omic data

openCyto: This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy.

paircompviz: This package provides visualization of the results from the multiple (i.e. pairwise) comparison tests such as pairwise.t.test, pairwise.prop.test or pairwise.wilcox.test. The groups being compared are visualized as nodes in Hasse diagram. Such approach enables very clear and vivid depiction of which group is significantly greater than which others, especially if comparing a large number of groups.

pathifier: Pathifier is an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample.

plethy: This package provides the infrastructure and tools to import, query and perform basic analysis of whole body plethysmography and metabolism data. Currently support is limited to data derived from Buxco respirometry instruments as exported by their FinePointe software.

ProCoNA: Protein co-expression network construction using peptide level data, with statisical analysis. (Journal of Clinical Bioinformatics 2013, 3:11 doi:10.1186/2043-9113-3-11)

prot2D: The purpose of this package is to analyze (i.e. Normalize and select significant spots) data issued from 2D GEl experiments

PSICQUIC: PSICQUIC is a project within the HUPO Proteomics Standard Initiative (HUPO-PSI). It standardises programmatic access to molecular interaction databases.

qcmetrics: The package provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats.

qusage: This package is an implementation the Quantitative Set Analysis for Gene Expression (QuSAGE) method described in (Yaari G. et al, Nucl Acids Res, 2013). This is a novel Gene Set Enrichment-type test, which is designed to provide a faster, more accurate, and easier to understand test for gene expression studies. qusage accounts for inter-gene correlations using the Variance Inflation Factor technique proposed by Wu et al. (Nucleic Acids Res, 2012). In addition, rather than simply evaluating the deviation from a null hypothesis with a single number (a P value), qusage quantifies gene set activity with a complete probability density function (PDF). From this PDF, P values and confidence intervals can be easily extracted. Preserving the PDF also allows for post-hoc analysis (e.g., pair-wise comparisons of gene set activity) while maintaining statistical traceability. Finally, while qusage is compatible with individual gene statistics from existing methods (e.g., LIMMA), a Welch-based method is implemented that is shown to improve specificity. For questions, contact Chris Bolen (cbolen1@gmail.com) or Steven Kleinstein (steven.kleinstein@yale.edu)

Rchemcpp: The Rchemcpp package implements the marginalized graph kernel and extensions, Tanimoto kernels, graph kernels, pharmacophore and 3D kernels suggested for measuring the similarity of molecules.

RDAVIDWebService: Tools for retrieving data from the Database for Annotation, Visualization and Integrated Discovery (DAVID) using Web Services into R objects. This package offers the main functionalities of DAVID website including: i) user friendly connectivity to upload gene/background list/s, change gene/background position, select current specie/s, select annotations, etc. ii) Reports of the submitted Gene List, Annotation Category Summary, Gene/Term Clusters, Functional Annotation Chart, Functional Annotation Table

rfPred: Based on external numerous data files where rfPred scores are pre-calculated on all genomic positions of the human exome, the package gives rfPred scores to missense variants identified by the chromosome, the position (hg19 version), the referent and alternative nucleotids and the uniprot identifier of the protein. Note that for using the package, the user has to be connected on the Internet or to download the TabixFile and index (approximately 3.3 Go).

Roleswitch: Infer Probabilities of MiRNA-mRNA Interaction Signature (ProMISe) using paired expression data from a single sample. Roleswitch operates in two phases by inferring the probability of mRNA (miRNA) being the targets (“targets”) of miRNA (mRNA), taking into account the expression of all of the mRNAs (miRNAs) due to their potential competition for the same miRNA (mRNA). Due to dynamic miRNA repression in the cell, Roleswitch assumes that the total transcribed mRNA levels are higher than the observed (equilibrium) mRNA levels and iteratively updates the total transcription of each mRNA targets based on the above inference.

RRHO: The package is aimed at inference on the amount of agreement in two sorted lists using the Rank-Rank Hypergeometric Overlap test.

RTN: This package provides classes and methods for transcriptional network inference and analysis. Modulators of transcription factor activity are assessed by conditional mutual information, and master regulators are mapped to phenotypes using different strategies, e.g., gene set enrichment, shadow and synergy analyses.

rTRM: rTRM identifies transcriptional regulatory modules (TRMs) from protein-protein interaction networks.

rTRMui: This package provides a web interface to compute transcriptional regulatory modules with rTRM.

seqCNA: Copy number analysis of high-throughput sequencing cancer data with fast summarization, extensive filtering and improved normalization

SeqVarTools: An interface to the fast-access storage format for VCF data provided in SeqArray, with tools for common operations and analysis.

shinyTANDEM: This package provides a GUI interface for rTANDEM. The GUI is primarily designed to visualize rTANDEM result object or result xml files. But it also provides an interface for creating parameter objects, launching searches or performing conversions between R objects and xml files.

SigFuge: Algorithm for testing significance of clustering in RNA-seq data.

SimBindProfiles: SimBindProfiles identifies common and unique binding regions in genome tiling array data. This package does not rely on peak calling, but directly compares binding profiles processed on the same array platform. It implements a simple threshold approach, thus allowing retrieval of commonly and differentially bound regions between datasets as well as events of compensation and increased binding.

SpacePAC: Identifies clustering of somatic mutations in proteins via a simulation approach while considering the protein’s tertiary structure.

spliceR: An R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.

spliceSites: Align gap positions from RNA-seq data

sRAP: This package provides a pipeline for gene expression analysis (primarily for RNA-Seq data). The normalization function is specific for RNA-Seq analysis, but all other functions (Quality Control Figures, Differential Expression and Visualization, and Functional Enrichment via BD-Func) will work with any type of gene expression data.

sSeq: The purpose of this package is to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation. The method of moment (MM) estimates for dispersion are shrunk towards an estimated target, which minimizes the average squared difference between the shrinkage estimates and the initial estimates. The exact per-gene probability under the NB model is calculated, and used to test the hypothesis that the expected expression of a gene in two conditions identically follow a NB distribution.

STRINGdb: The STRINGdb package provides a user-friendly interface to the STRING protein-protein interactions database ( http://www.string-db.org ).

supraHex: A supra-hexagonal map is a giant hexagon on a 2-dimensional grid seamlessly consisting of smaller hexagons. It is supposed to train, analyse and visualise a high-dimensional omics data. The supraHex is able to carray out gene/meta-gene clustering and sample correlation, plus intuitive visualisations to facilitate exploratory analysis. Uniquely to this package, users can simultaneously understand their own omics data in a sample-specific fashion but without loss of information on large genes.

SwimR: SwimR is an R-based suite that calculates, analyses, and plots the frequency of C. elegans swimming behavior over time. It places a particular emphasis on identifying paralysis and quantifying the kinetic elements of paralysis during swimming. Data is input to SwipR from a custom built program that fits a 5 point morphometric spine to videos of single worms swimming in a buffer called Worm Tracker.

TargetScore: Infer the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores. Variaitonal Bayesian Gaussian mixture model (VB-GMM) is applied to log fold-changes and sequence scores to obtain the posteriors of latent variable being the miRNA targets. The final targetScore is computed as the sigmoid-transformed fold-change weighted by the averaged posteriors of target components over all of the features.

TCC: This package provides a series of functions for performing differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization to obtain a well-ranked gene list where true DEGs are top-ranked and non-DEGs are bottom ranked. This can be done by performing a multi-step normalization strategy (called DEGES for DEG elimination strategy). A major characteristic of TCC is to provide the robust normalization methods for several kinds of count data (two-group with or without replicates, multi-group/multi-factor, and so on) by virtue of the use of combinations of functions in other sophisticated packages (especially edgeR, DESeq, and baySeq).

TFBSTools: Software package for TFBS.

tRanslatome: Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions (treated vs. untreated, diseased vs. normal, mutant vs. wild-type) among different levels of gene expression (transcriptome ,translatome, proteome), using several statistical methods: Rank Product, t-test, SAM, Limma, ANOTA, DESeq, edgeR. Possibility to plot the results with scatterplots, histograms, MA plots, standard deviation (SD) plots, coefficient of variation (CV) plots. Detection of significantly enriched post-transcriptional regulatory factors (RBPs, miRNAs, etc) and Gene Ontology terms in the lists of DEGs previously identified for the two expression levels. Comparison of GO terms enriched only in one of the levels or in both. Calculation of the semantic similarity score between the lists of enriched GO terms coming from the two expression levels. Visual examination and comparison of the enriched terms with heatmaps, radar plots and barplots.

trio: Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data.

vtpnet: variant-transcription factor-phenotype networks, inspired by Maurano et al., Science (2012), PMID 22955828

XVector: Memory efficient S4 classes for storing sequences “externally” (behind an R external pointer, or on disk).

NEWS from new and existing packages

Package maintainers can add NEWS files describing changes to their packages. The following package NEWS is available:

ADaCGH2

Changes in version 2.1.6 (2013-09-23):

Started testing against R beta 3.0.2. Fixed Imports and Depends.
chromData: using “short”, not “ushort”, to catch more user errors.
pSegmentGLAD: using a custom daglad that minimizes unneeded calls, specially sorting, that can be very expensive.
Added “certain_noNA” to segmentation methods.
Started testing against R-devel (to become R-3.1.0).

Changes in version 2.1.5 (2013-09-16):

Fixed typos.
Minimized usage of “:::”, removed unused functions for Ansari, and some assignemts that no longer made sense (all packages now have namespaces).
Minimize “Depends” and use “Suggests” and “Imports” in DESCRIPTION with “importFrom” in NAMESPACE.
No longer using our own mergeLevels, since identical to the ones in aCGH package.
GLAD uses now the recommended fastest option (smoothfunc=haarseg).

Changes in version 2.1.4 (2013-07-01):

Fixed missing entry in bib of vignette.

Changes in version 2.1.3 (2013-06-20):

Default merging of pSegmentDNAcopy changed to “MAD”, to reflect our usage.
Added more benchmarking results and recommendations to the vignette, and fixed some typos.

Changes in version 2.1.2 (2013-06-17):

More changes in cutFile to try and get it to run under Mac.
Fixed names in long examples that were leading to mistakenly reporting results as different.
Added new benchmarking results.

Changes in version 2.1.1 (2013-06-16):

Many small changes and adaptations in vignette and help to get it to work unded Win and Mac.
Changes in cutFile to try and get it to run under Mac.

Changes in version 2.1.0 (2013-05-30):

This is a major rewrite of a most of the code, has new functions, major changes in existing functions, new vignettes, etc.
We no longer use snowfall.
Major changes in parallelization, using forking.
Reading of data: many more options, parallelized reading.

affxparser

Changes in version 1.34.0 (2012-10-14):

The version number was bumped for the Bioconductor release version, which is now Bioc v2.13 for R (>= 3.0.0).

Changes in version 1.33.4 (2013-09-23):

SPEEDUP/CLEANUP: Package now uses which() instead of whichVector() of ‘R.utils’. Before R (< 2.11.0), which() used to be 10x slower than whichVector(), but now it’s 3x faster.

Changes in version 1.33.3 (2013-06-29):

Same updates as in release v1.32.3.

Changes in version 1.33.2 (2013-05-25):

Same updates as in release v1.32.2.

Changes in version 1.33.1 (2013-05-20):

Same updates as in release v1.32.1.

Changes in version 1.33.0 (2013-04-03):

The version number was bumped for the Bioconductor devel version.
No updates.

Changes in version 1.32.3 (2013-06-29):

BUG FIX: Since affxparser v1.30.2/1.31.2 (r72352; 2013-01-08), writeCdf() would incorrectly encode the unit types, iff the input ‘cdf’ argument specified them as integers, e.g. as done by writeCdf() for AffyGenePDInfo in aroma.affymetrix. More specifically, the unit type index would be off by one, e.g. an ‘expression’ unit (1) would be encoded as an ‘unknown’ unit (0) and so on. On the other hand, if they were specified by their unit-type names (e.g. ‘expression’) the encoding should still be correct, e.g. if input is constructed from readCdf() of affxparser. Thanks to Guido Hooiveld at Wageningen UR (The Netherlands) for reporting on this.
BUG FIX: Similarily, writeCdf() has “always”, at least affxparser v1.7.4 since (r21888; 2007-01-09), encoded unit directions and QC unit types incorrectly, iff they were specified as integers.

Changes in version 1.32.2 (2013-05-25):

SPEEDUP: Removed all remaining gc() calls.
SPEEDUP: Replaced all rm() calls with NULL assignments.

Changes in version 1.32.1 (2013-05-20):

CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.

annmap

Changes in version 1.2.1:

BUG ANNMAP-112 transcriptCoordsToGenome and proteinCoordsToGenome both failed when returning a GRanges object as I had strand as a numeric, rather than an integer.

AnnotationHub

Changes in version 1.2.0:

NEW FEATURES

Support for TabixFile VCF files

BUG FIXES

incorrect tab completion does not reset the completion line

aroma.light

Changes in version 1.32.0 (2012-10-14):

The version number was bumped for the Bioconductor release version, which now is Bioc v2.13 for R (>= 3.0.0).

Changes in version 1.31.10 (2013-10-08):

Added averageQuantile() for matrices in addition to lists.
SPEEDUP: Now normalizeQuantileSpline(…, sortTarget=TRUE) sorts the target only once for lists of vectors just as done for matrices.
DOCUMENTATION: Merged the documentation for normalizeQuantileSpline() for all data types into one help page. Same for plotXYCurve().
BUG FIX: Argument ‘lwd’ of plotXYCurve(X, …) was ignored if ‘X’ was a matrix.
Bumped up package dependencies.

Changes in version 1.31.9 (2013-10-07):

Now library(aroma.light, quietly=TRUE) attaches the package completely silently without any messages.
Now the ‘aroma.light’ Package object is also available when the package is only loaded (but not attached).
DOCUMENTATION: Merged the documentation for normalizeQuantileRank() for numeric vectors and lists.
DOCUMENTATION: Now documention S3 methods under their corresponding generic function.

Changes in version 1.31.8 (2013-10-02):

DOCUMENTATION: More generic functions are now “aliased” under relevant corresponding methods.

Changes in version 1.31.7 (2013-09-27):

SPEEDUP: Now all package functions utilizes ‘matrixStats’ functions where possible, e.g. anyMissing(), colMins(), and rowWeightedMedians().
Bumped up package dependencies.

Changes in version 1.31.6 (2013-09-25):

CLEANUP: Package no longer use a fallback attachment of the ‘R.oo’ package upon attachment.

Changes in version 1.31.5 (2013-09-23):

ROBUSTNESS: Now properly declaring all S3 methods in the NAMESPACE file.
SPEEDUP/CLEANUP: normalizeTumorBoost() now uses which() instead of whichVector() of ‘R.utils’. Before R (< 2.11.0), which() used to be 10x slower than whichVector(), but now it’s 3x faster.
CLEANUP: Now only using ‘Authors@R’ in DESCRIPTION, which is possible since R (>= 2.14.0). Hence the new requirement on the version of R.
Bumped up package dependencies.

Changes in version 1.31.4 (2013-09-10):

CLEANUP: Now package explicitly imports what it needs from matrixStats.
Bumped up package dependencies.

Changes in version 1.31.3 (2013-05-25):

SPEEDUP: Removed all remaining gc() calls, which were in normalizeQuantileSpline().
SPEEDUP: Replaced all rm() calls with NULL assignments.
Updated the package dependencies.

Changes in version 1.31.2 (2013-05-20):

Same updates as in v1.30.2.

Changes in version 1.31.1 (2011-04-18):

Same updates as in v1.30.1.

Changes in version 1.31.0 (2013-04-03):

The version number was bumped for the Bioc devel version.

Changes in version 1.30.5 (2013-09-25):

Backport from v1.31.5: Declaring all S3 methods in NAMESPACE.
Backport from v1.31.5: normalizeTumorBoost() now uses which(), which also removes one dependency on ‘R.utils’.

Changes in version 1.30.4 (2013-09-25):

Backport from v1.31.4: Now package explicitly imports what it needs from matrixStats.

Changes in version 1.30.3 (2013-09-25):

Backport from v1.31.3: Removal of all gc() calls and removal of variables is now faster.
Removed one stray str() debug output in robustSmoothSpline().

Changes in version 1.30.2 (2013-05-20):

CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.

Changes in version 1.30.1 (2013-04-18):

Now backtransformPrincipalCurve() preserves dimension names.
BUG FIX: backtransformPrincipalCurve() gave an error if the pricipal curve was fitted using data with missing values.
BUG FIX: fitPrincipalCurve() would not preserve dimension names if data contain missing values.

ASSET

Changes in version 1.0:

USER VISIBLE CHANGES

Initial release of the ASSET package.

BUG FIXES

None.

PLANS

The next release will have new features for h.traits and h.types.

BAGS

Changes in version 2.1:

Considering on having a function for time series data.

BaseSpaceR

Changes in version 1.1:

NEW FEATURES

New high level function performOAuth() makes the App authentication easier.
initializeAuth() now fires up a browser window and starts the OAuth v2 process. Users can use ‘useBrowser’ parameter to control this behaviour.

SIGNIFICANT USER-VISIBLE CHANGES

requestAccessToken() now returns an integer giving the status of request: * 1 if the request was succesful and an access_token was received * -1 if the AppAuth handle already contains a feasible access token * An integer larger than one if the request fails. There is also a new ‘verbose’ parameter controling the messages shown to the user. By default ‘verbose = TRUE’

BUG FIXES

Added end of line character to some messages.
fileItem$Size is now stored as a numeric, thus allowing for file larger than 2GB.

BiGGR

Changes in version 0.99.3:

Initial release of BiGGR in Bioconductor. Package was formerly available on CRAN.

bigmemoryExtras

1.3.1: # Thu 06-20-2013 - 11:29

1.4.0: # Wed 06-26-2013 - 19:56

1.4.1:

bioassayR

Changes in version 1.0.0 (2013-10-15):

NEW FEATURES

Provides a pre-built database containing PubChem Bioassay bioactivity data from hundreds of thousands of assays

NEW FEATURES

Features for identifying target selective compounds

NEW FEATURES

Features for identifying druggable protein targets

NEW FEATURES

S4 classes and database structure for large bioactivity data

Biobase

Changes in version 2.21:

USER VISIBLE CHANGES

channelNames<-,NChannelSet,*-methods allow re-naming channels

USER VISIBLE CHANGES

NChannelSet validity requires all assayDataElementNames() to be levels in varMetadata()$channel.

BiocParallel

Changes in version 0.99.0:

NEW FEATURES

mclapply(), pvec() require only length, [, and (for mclapply) [[.
pvectorize() creates a parallel version of its vectorized function argument.
MulticoreParam, SnowParam, DoparParam (foreach-derived), SerialParam to parameterize back-ends.
bplapply, bpvec as parallel evaluation models.
bpstart, bpstop, bpisup for back-end management.
bpvec has a new argument AGGREGATE, a function to specify how results are to be combined.

SIGNIFICANT USER-VISIBLE CHANGES

BPPARM is now used as the argument name for passing BiocParallelParam instances to functions.
bplapply and bpvec now only dispatch on X and BPPARAM.

BiocStyle

Changes in version 1.0.0:

USER VISIBLE CHANGES

Rename \Rpkg{} as \CRANpkg{} to reflect functionality

BUG FIXES

avoid option conflict with \usepackage{colors}

biomvRCNS

Changes in version 1.1.9:

BUG FIXES

NA bug when model fails

BUG FIXES

using the length of the segment if shorter than maxk

Changes in version 1.1.8:

NEW FEATURES

add error catching in biomvRhsmm

BUG FIXES

updates in package vignette

NEW FEATURES

fine tuning of memory usage for large count data structure

BUG FIXES

minor bug fixes

Changes in version 1.1.7:

NEW FEATURES

add support of Rle like sparse data in mcols of large count data structure.

NEW FEATURES

add mclapply for parallel processing of different seqnames in biomvRhsmm

Changes in version 1.1.6:

BUG FIXES

fix nbinom emis estimateSegCommonDisp -> nbinomCLLDD

Changes in version 1.1.5:

NEW FEATURES

update biomvRGviz to have trackList returned when tofile=FALSE

BUG FIXES

typo fix in function argument

Changes in version 1.1.4:

NEW FEATURES

update biomvRGviz to plot multiple samples in one, and more param
plot method now defaults to multiple samples in one, sampleInOne=T

BUG FIXES

fix states rank when prior.m=cluster

Changes in version 1.1.3:

NEW FEATURES

the x slot in the returning object for biomvRhsmm now also contains the probability of associated state for each position

NEW FEATURES

the param slot in the returning object for biomvRhsmm now also contains the updated emission and sojourn parameters for each seqname and sample column

Changes in version 1.1.2:

NEW FEATURES

add a new clustering method for emission prior estimation
add a new example section of DMR detection in the vignette

BUG FIXES

switch off several data checking warnings, use normal cat() instead

Changes in version 1.1.1:

NEW FEATURES

add support of direct input of sojourn parameters as named list.

BUG FIXES

suppress warnings generated when appending GRanges object for the output

BitSeq

Changes in version 1.5.5 (2013-10-12):

BUG FIXES

fixed problem with processing Fasta reads

BUG FIXES

fixed problem with processing mixed alignments in empirical estimation

BUG FIXES

use proper includes for samtools

Changes in version 1.5.2 (2013-10-09):

BUG FIXES

fixed force option in estimateHyperPar (it worked the wrong way around)
fixed problem with effective lengths being too small

NEW FEATURES

add estimateVBExpression function that uses Variational Bayes inference method to estimate expression levels of transcripts

Changes in version 1.4.3 (2013-07-08):

BUG FIXES

fixed major bug in getGeneExpression and getWithinGeneExpression that caused wrong results for some genes if transcripts were not grouped by genes

NEW FEATURES

fixed bug in parseAlignment which would occasionally cause underflow in effective length computation

BUG FIXES

fixed taking square root of wrong column in getExpression result’s $means field

NEW FEATURES

much faster parseAlignment computation

BUG FIXES

improved precision in getGeneExpression and getWithinGeneExpression

NEW FEATURES

getWithinGeneExpression provides option to keep transcripts in original order even if they are not grouped by genes

bsseq

Changes in version 0.9:

Fixed a problem with “width” in the title of bsseq plots.
plot.BSseqTstat now allows for BSseqTstat objects computed without correction.
validObject(BSseq) has been extended to also check for sampleNames consistency.
Fixed a bug related to validity checking.
Increased maxk from 10,000 to 50,000 in calls to locfit, to allowing fitting the model on genomes with unusally long chromosomes (Thanks to Brian Herb for reporting).
The class representation for class ‘BSseq’ has changed completely. The new class is build on ‘SummarizedExperiment’ from GenomicRanges instead of ‘hasGRanges’. Use ‘x <- updateObject(x)’ to update serialized (saved) objects.
Fixing a problem in orderBSseq related to chromosome names.
Allowed user specification of maxk, with a default of 10,000 in BSmooth.
Many bugfixes made necessary by the new class representation.
Better argument checking in BSmooth.tstat.
A few undocumented functions are now documented.
Rewrote orderBSseq

bumphunter

Changes in version 1.1:

Added NEWS file.
Fixed a bug related to >= for numerics.
Added smoothing using a gaussian kernal as implemented in the locfit package through the function locfitByCluster.
Added closeSockets for cleanup for doParallel on Windows.
More bugfixes for windows; now using foreachCleanup().
Added a ‘bumps’ class and print method.
annotateNearest / regionMatch now give NA annotations for queries with no nearest subject (perhaps because the seqname is missing from the subject). Previously this was taken to be mistaken input and a hard error raised.
Speedup of fwer computations using foreach.
Added boundedClusterMaker.
bug fix to internal function .getModT (which are not used in the main bumphunter functions). Now the t-statistics returned a correct.

CAMERA

Changes in version 2012-06-12:

Bugfix in findIsotopes, clears ‘vec’ must be sorted non-decreasingly error

Changes in version 2012-06-11:

Version 1.13.4
Add ByteCompile: TRUE
Bugfix for findIsotopes, clears subscript out of bound error

Changes in version 2012-05-25:

Version 1.13.2
First changes for improved isotope detection

Changes in version 2012-04-12:

Version 1.13.1
Bugfix for findIsotopes to fix not consecutive isotope label like [M]+,[M+2]+ without [M+1]+

Changes in version 2012-03-19:

Version 1.11.10
Bugfix in groupCorr, where the function throws an error if argument xraw is not null
Version 1.11.9
Bugfix in findAdducts, where adduct annotation filtering was to stringent, if ips score is higher 1.5

Changes in version 2012-02-29:

Version 1.11.8
Bugfix in findAdducts parallel mode, where wrong psgrp indices were stored in annoGrp

Changes in version 2012-02-17:

Version 1.11.7
Bugfix in findAdducts, where the ruleset is not saved within a xsAnnotate object with user defined rules
Changed a general groupCorr behaviour. If no edge is above correlation threshold, all peaks are seperated in pspecs of size 1

Changes in version 2012-02-15:

Version 1.11.6
Fix error in groupCorr: If sample is set to something other than 1 or NA, it result in a crash

Changes in version 2012-02-10:

Version 1.11.5
Bugfix in groupCorr where parameter cor_eic_th doesn’t influence correlation across samples
Add new parameter for groupCorr cor_exp_th

Changes in version 2011-29-11:

Version 1.11.3
Add new function combinexsAnnos. It allows checking and reannotation of sample with a coressponding sample from the opposite ion mode

Changes in version 2011-28-04:

Fix bug in getpspectra, which incorrect label isotope peaks

Changes in version 2011-24-11:

Version 1.11.2
Bugfix in annotateDiffreport: Since 1.7.7 mismatch of the peaklist from CAMERA and the diffreport function results in false ordered peaktable

Changes in version 2011-24-05:

Fix bug in findIsotopes, which could cause a crash, if maxiso was higher than 3

Changes in version 2011-23-09:

Version 1.9.7
Bugfix in calcIsotopes, causes groupCorr with calcIso to crash with (Error in rbind(resMat …)
Bugfix in groupCorr with given xcmsRaw

Changes in version 2011-22-08:

Version 1.9.6
Bugfix in plotEICs (Error in pks[, 1] : incorrect number of dimensions)

Changes in version 2011-20-25:

Version 1.9.9
added some “drop=FALSE” to fix “Error in isomatrix[, 1] : incorrect number of dimensions” error

Changes in version 2011-20-10:

Version 1.9.8
Correct rule table extended_adducts_pos.csv (typo in proton mass)

Changes in version 2011-12-12:

Version 1.11.4
Add missing Rd page combinexsAnnos

Changes in version 2011-12-05:

plotPsSpectrum now accepts additional parameters for plot

Changes in version 2011-10-11:

Version 1.11.1
add the possibility to extract multiple isotope intensity from different samples with getIsotopeCluster

Changes in version 2011-04-04:

Fix bug in findAdducts, if pseudospectrum mass list has only NA values

Changes in version 2011-02-08:

Version 1.9.5
Bugfix for findIsotopes if ppm was very high it could occur that one peak is assigned as two or more isotope peaks
Version 1.9.4
Add parameter polarity to xsAnnotate constructor
getPeaklist and getpspectra returns now correct annotation of negative charged ions [M]-
Add snow as additonal possibilty for parallel processing
Add function cleanParallel to clean up with spawned slave processes

Changes in version 2010-29-09:

Add function findNeutralLoss and findNeutralLossSpecs

Changes in version 2010-23-11:

Fix bug in findAdducts. Function failed, if run in parallel mode.

Changes in version 2010-20-09:

Add function getIsotopeCluster for retrival of isotope cluster

Changes in version 2010-11-10:

Rewrite Vignette

Changes in version 2010-11-06:

Speed up in findAdducts
Fix unit tests

Changes in version 2010-08-11:

Add intval parameter to groupFWHM and findIsotopes
Change getPeaklist to S4 Methods.
Add getPeaklist parameter intval, where the intensity value can be selected
Additional bugfix for findIsotopes. Could occur with 1.7.1, that all isotopes will be deleted.

Changes in version 2010-05-03:

Fix bug in findIsotopes, crashed with dim error

Changes in version 2010-04-20:

Fix bug in annotate function

Changes in version 2010-04-19:

Last changes for the next BioC release
Rewrite of the vignette

Changes in version 2010-03-17:

Hugh changes in CAMERA for working with multiple sample
Add check constrains in groupCorr for isotopes and primary adducts

Changes in version 2010-01-11:

Fix bug in findIsotopes. Occurs if the first isotope peak, could be assigned from two different monoisotopic peaks.
Reduce slightly the number of found isotopes

Changes in version 2009-11-24:

Add experimental parallel mode with MPI

Changes in version 2009-11-20:

Fix bug in setting ruletable

Changes in version 2009-08-26:

add nSlaves as argument to findAdducts (for parallel annotation with MPI)

Changes in version 2009-08-24:

small bugfixes in getPeaklist
add neutral losses to rule set

Changes in version 2009-08-12:

Fixed plotEICs for 1 peak groups

Changes in version 2009-08-04:

Add ips Score to annoGrp

Changes in version 2009-06-03:

Add adduct labels to plotPeaks()
Add adduct labels to plotEICs()

Changes in version 2009-05-22:

Add first visualisation function plotEICs() and plotPeaks()

Changes in version 2009-05-06:

bump for devel 2.5

Changes in version 2009-03-30:

add combine_xsanno
small refactoring
changes in scoring schemata

Changes in version 2009-03-18:

after groupCorr every peak is now member of a group
bugfix: remove xM-xH clones
remove dependency on Hmisc

Changes in version 2009-03-10:

speed-up of findAdducts

Changes in version 2009-02-24:

refactoring findAdducts
add methods for pos/neg polarity comparison

Changes in version 2009-02-20:

replace na.omit with naOmit

Changes in version 2009-02-18:

add neutral losses into ruleset
other bugfixes

Changes in version 2009-01-19:

Change isotope nomination
add lists for fragments, ions and neutral losses

Changes in version 2008-10-15:

Lot of bugfixes and speed up the correlation

Changes in version 2008-10-13:

First build for version 0.1.1

Changes in version 2007-10-12:

Inital release & collection of stuff

categoryCompare

1.5.1:

CellNOptR

Changes in version 1.8.0 (2013-08-28):

BUG FIX
- readMIDAS: DV, DA and TR can now be in the specy name
- prep4sim can read self loop
- plotOptimResultsPan: fix special cases with one or no inhibitors/stimuli
- fix bug in cutNONC: notMat was not populated
- readSIF: can read and gates coded in big caps as well as small ones
- writeMIDAS: manages absence of inhibitors
CHANGES
- CNOlist: subfield parameter has been removed. Subfield are automatically found from the header
- expandAndGates are not limited to 4 inputs anymore
- normaliseCNOlist: EC50 is set to 1 by default
NEW FEATURES
- readSBMLQual: a function to read prior knowledge network in SBMLqual format. !! This is a prototype. use with care for now.
- cutCNOlist function can cut a MIDAS file over time

ChemmineOB

Changes in version 1.0.0:

NEW FEATURES

functions to convert between any two formats supported by OpenBabel

NEW FEATURES

descriptor computation

NEW FEATURES

fingerprint computation

chimera

Changes in version 1.3.15:

NEW FEATURES

GapFiller Nadalin et al BMC Bioinformatics was implemented as de novo validation tool for fusion break point.

Changes in version 1.3.12:

NEW FEATURES

Picard-tools can be downloaded in chimara folder, picardInstallation.

NEW FEATURES

The wrapper function validateSamFile uses picard tools to validate SAM/BAM files.

NEW FEATURES

The wrapper function filterSamReads allows SAM and BAM filtering.

Changes in version 1.3.9:

NEW FEATURES

Rsubread aligner is used instead of tophat.

Changes in version 1.3.3:

NEW FEATURES

STAR fusion import function: importFusionData

NEW FEATURES

STAR run function: starInstallation

NEW FEATURES

STAR installation function: starRun

NEW FEATURES

BiocParallel supported functions: STAR import fusionName supportingReads filterList

chipenrich

Changes in version 1.0:

PKG FEATURES

chipenrich performs gene set enrichment tests on peaks called from a ChIP-seq experiment

PKG FEATURES

chipenrich empirically corrects for confounding factors such as the length of genes and mappability of sequence surrounding genes

PKG FEATURES

Use multiple definitions of a gene “locus” when testing for enrichment, or provide your own definition

PKG FEATURES

Test for enrichment using chipenrich or Fisher’s exact test (should only be used for datasets where peaks are close to TSSs, see docs)

PKG FEATURES

Test multiple sets of genesets (Gene Ontology, KEGG, Biocarta, OMIM, etc.)

PKG FEATURES

Multiple plots to describe binding distance and likelihood of a peak as a function of gene length

PKG FEATURES

Support for human (hg19), mouse (mm9), and rat (rn4) genomes

PKG FEATURES

Many conveniences such as seeing which peaks were assigned to genes, their position relative to those genes and their TSS, etc.

PKG FEATURES

See how many peaks were assigned to each gene along with the length and mappability of the gene

Changes in version 0.99.2:

USER-VISIBLE CHANGES

Updated examples for various functions to be runnable (removed donttest)
Updated DESCRIPTION to use Imports: rather than Depends:
Updated license to GPL-3
Updated NEWS file for bioconductor guidelines

BUG FIXES

Added a correction for the case where a small gene set has a peak in every gene. This has the result of making a very few number of tests slightly conservative, at the benefit of actually being able to return a p-value for them.

Changes in version 0.99.1:

USER-VISIBLE CHANGES

Minor updates to documentation for Bioconductor

Changes in version 0.99.0:

NEW FEATURES

Initial submission to Bioconductor

Changes in version 0.9.6:

NEW FEATURES

Added peaks per gene as a returned object / output file

Changes in version 0.9.5:

BUG FIXES

Update to handle bioconductor/IRange’s new “functionality” for distanceToNearest and distance

USER-VISIBLE CHANGES

Changed sorting of results to put enriched terms first (sorted by p-value), then depleted (also sorted by p-value)

Changes in version 0.9.4:

USER-VISIBLE CHANGES

Minor changes to vignette and documentation

Changes in version 0.9.3:

NEW FEATURES

Addition of rat genome

BUG FIXES

chipenrich() will correctly open both .bed and .bed.gz files now

Changes in version 0.9.2:

NEW FEATURES

Added ability for user to input their own locus definition file (pass the full path to a file as the locusdef argument)
Added a data frame to the results object that gives the arguments/values passed to chipenrich, also written to file *_opts.tab
For FET and chipenrich methods, the outcome variable can be recoded to be >= 1 peak, 2 peaks, 3 peaks, etc. using the num_peak_threshold parameter
Added a parameter to set the maximum size of gene set that should be tested (defaults to 2000)

USER-VISIBLE CHANGES

Previously only peak midpoints were given in the peak –> gene assignments file, now the original peak start/ends are also given
Updated help/man with new parameters and more information about the results

BUG FIXES

Fixed an issue where status in results was not enriched if the odds ratio was infinite, and depleted if the odds ratio was exactly zero

Changes in version 0.9.1:

NEW FEATURES

Added a QC plot for expected # of peaks and actual # of peaks vs. gene locus length. This will be automatically created if qc_plots is TRUE, or the plots can be created using the plot_expected_peaks function.

NEW FEATURES

Distance to TSS is now signed for upstream (-) and downstream (+) of TSS

NEW FEATURES

Column added to indicate whether the geneset is enriched or depleted

Changes in version 0.9:

NEW FEATURES

Added support for reading BED files natively

BUG FIXES

Fixed bug where invalid geneset in chipenrich() wasn’t detected properly

Changes in version 0.8:

BUG FIXES

Fixed crash when mappability contained an NA (will be removed from DB in future version)

Changes in version 0.7:

USER-VISIBLE CHANGES

Updated binomial test to sum gene locus lengths to get genome length and remove genes that are not present in the set of genes being tested
Updated spline fit plot to take into account mappability if requested (log mappable locus length plotted instead of simply log locus length)
Removed SAMPLEABLE_GENOME* constants since they are no longer needed
Updated help files to reflect changes to plot_spline_length and chipenrich functions

BUG FIXES

Fixed bug where results for multiple gene set types (e.g. doing BioCarta and KEGG together) were not sorted by p-value

Changes in version 0.6:

BUG FIXES

Fixed bug where 1kb/5kb locusdefs could fail if not all peaks were assigned to a gene

Changes in version 0.5:

USER-VISIBLE CHANGES

Updated help to explain new mappability model

USER-VISIBLE CHANGES

Changed how mappability is handled - now multiplies gene locus length by mappability, rather than adjusting as a spline term

ChIPpeakAnno

Changes in version 2.9.6:

BUG FIXES

Change Enhancer.Silencer to intergenic.Region in assignChromosomeRegion.

Changes in version 2.9.5:

BUG FIXES

fixed bug error in negative widths are not allowed when call findOverlappingPeaks.

cisPath

Changes in version 1.1.6:

Fix a bug

Changes in version 1.1.5:

documentation improvements

Changes in version 1.1.4:

Fix a bug

Changes in version 1.1.3:

documentation improvements

Changes in version 1.1.2:

Fix a bug

Changes in version 1.1.1:

Several methods have been added to format PPI data downloaded from PINA and STRING databases

cleaver

Changes in version 0.99.5 (2013-07-24):

vignette:
remove duplicated sessionInfo entries.

Changes in version 0.99.4 (2013-07-23):

vignette:
use BiocStyle.
add sessionInfo() and TOC.

Changes in version 0.99.3 (2013-07-08):

vignette: add second BRAIN reference.

Changes in version 0.99.2 (2013-06-17):

Replace own AAStringSetList constructor by Biostrings::AAStringSetList.
man/cleaver-package.Rd: remove static date.
vignette: add dynamic date and don’t load Biostrings manually anymore.
NAMESPACE: don’t import from Biostrings and IRanges.

Changes in version 0.99.1 (2013-05-30):

Add S4-methods for character, AAString, AAStringSet.
man/cleave-methods.Rd: split table of cleavage rules to reduce table width.
Extend vignette (add BRAIN and UniProt.ws based examples).

Changes in version 0.99.0 (2013-04-27):

Initial release.

clonotypeR

Changes in version 2013-10-07:

Commited 0.99.6 to Bioconductor.
Added unit tests for yassai_identifier().

Changes in version 2013-08-01:

Unified the syntax of common_clonotypes and unique_clonotypes.

Changes in version 2013-05-07:

Resubmitted 0.99.5 to Bioconductor.
Distribute a copy of the clonotypes extracted from example_data.
Execute all examples in the vignette.

Changes in version 2013-05-01:

Resubmitted 0.99.4 to Bioconductor
Moved the Markdown vignette to ‘/vignettes’.
Added executable example with test data to the vignette.

Changes in version 2013-04-26:

Resubmitted 0.99.3 to Bioconductor
Moved extra data to ‘inst/extdata’.
Moved the Markdown vignette to ‘inst/vignettes’.

Changes in version 2013-04-15:

Resubmission after correcting yassai_identifier() and other warnings.

Changes in version 2013-01-08:

Leaner Bioconductor package, without the wiki documentation. 2012-….. Charles Plessy plessy@riken.jp
Many entries missing.

Changes in version 2012-10-10:

Corrected Frenglish “improductive” with “unproductive”. This can break backwards compatibility.

Changes in version 2012-09-06:

Initial release

clusterProfiler

Changes in version 1.9.4:

bug fixed of readGff, add default parameter fill=TRUE in read.table function <2013-07-09, Mon>

Changes in version 1.9.3:

extend enrichGO to support 20 species <2013-07-09, Mon>
update vignettes. <2013-07-09, Mon>

Changes in version 1.9.1:

enrichGO and enrichKEGG support rat organism <2013-05-20, Mon>
change some code according to DOSE <2013-03-27, Wed>
modify enrichGO and enrichKEGG according to the change of enrich.internal, remove qvalueCutoff parameter, add pAdjustMethod, add universe paramter for user to specify background. <2013-05-29, Wed>
add function viewKEGG for visualizing KEGG pathway and update vignette. <2013-06-14, Fri>

CNAnorm

1.7.1:

CNORfuzzy

Changes in version 1.4.0:

cSimulator handles non integers values for the ihibitors and stimuli
gaDiscreteT1.R: fix issue when only 1 model was returned within tolerance
reduceFuzzy.R fix bug that causes seg faut (model was not cut properly)
defaultParametersFuzzy.R: added nTF to set number of TF to arbitrary value (not tested)
CNORwrapFuzzy.R: fixed pMutation argument that was not populated
gaDiscrete functions return best score as well in the dataframe.
output names of the fields returned by gaDiscrete are now using camel lower case so that plotFit from CellNoptR can be used
add C simulator

codelink

Changes in version 1.30.0:

The most visible change is that the CodelinkSet interface has been adopted as the official supported system. Documentation of these topic has been improved, and a new vignette describing the CodelinkSet system is available (Codelink_Introduction). Documentation to the old Codelink class has moved to the Codelink_Legacy vignette.
Before, readCodelink() would assign NA values to spots flagged as M (MSR spot), I (Irregular) and C (Contaminated). This could cause in large datasets that many spots would have at least one sample with NA at random, reducing drastically the number of de facto spots/probes used during normalization. Many thanks to Emmanuelle Dantony for spotting this problem and subsequent feedback. Because of this and other problems implementing and appropriate method to deal with this, automatic assigment of NA values is not performed anymore. The only exception are M flagged spots, which have intensity values of -9999, and hence do not represent any measure of intensity. Also, background and normalization methods are applied calling the appropriate functions in the limma package. Support for type- and flag-based weights has been included, and weights are automatically created by readCodelinkSet(). Weights can be used to modulate the contribution of some probes to normalization and during linear modeling more efficiently. Examples on how to use these approaches are documented in the vignette Codelink_Introduction.
Added generic method normalize() for Codelink and CodelinkSet classes.

DART

Changes in version 1.7.1:

Dependency changed from igraph0 to igraph (>=0.6.0) due to archiving of igraph0. In file PruneNet.R, the use of clusters() output was modified from zero-index to one-index accordingly.

deepSNV

Changes in version 1.99.3 (2013-07-25):

Updates

A few changes to shearwater vignette
Renamed arguments pi.gene and pi.backgr in makePrior()

Bugfixes

Fixed bug in bf2Vcf() when no variant is called

Changes in version 1.99.2 (2013-07-11):

Updates

Updated CITATION
Added verbose option to bam2R to suppress output
Changed mode() to “integer” for value of loadAllData()

Bugfixes

Fixed bug when only one variant is called in bf2Vcf()

Changes in version 1.99.1 (2013-06-25):

Updates

Using knitr for prettier vignettes

Bugfixes

Including shearwater vignette

Updates

fixed issues with deletions in bf2Vcf()

Bugfixes

makePrior() adds background on all sites

Changes in version 1.99.0 (2013-04-30):

Updates

New shearwater algorithm

Updates

Including VCF output through summary(deepSNV, value=”VCF”)

Changes in version 1.7.4 (2013-09-28):

Updates

Only using the Dirichlet prior for control

Updates

Change back version numbers from 1.99.x to 1.7.x (2.0 not quite there :)

deltaGseg

Changes in version 1.1.3:

corrected errors generated in denoiseSegments when segments are too small
refined plotting with data that has many subpopulations (>10)
more robust argument selection in functions

DESeq2

Changes in version 1.1.32:

By default, use QR decomposition on the design matrix X. This stabilizes the GLM fitting. Can be turned off with the useQR argument of nbinomWaldTest() and nbinomLRT().
Allow for “frozen” normalization of new samples using previous estimated parameters for the functions: estimateSizeFactors(), varianceStabilizingTransformation(), and rlogTransformation(). See manual pages for details and examples.

Changes in version 1.1.31:

The adjustment of p-values and use of Cook’s distance for outlier detection is moved to results() function instead of nbinomWaldTest(), nbinomLRT(), or DESeq(). This allows the user to change parameter settings without having to refit the model.

Changes in version 1.1.24:

The results() function allows the user to specify a contrast of coefficients, either using the names of the factor and levels, or using a numeric contrast vector. Contrasts are only available for the Wald test differential analysis.

Changes in version 1.1.23:

The results() function automatically performs independent filtering using the genefilter package and optimizing over the mean of normalized counts.

Changes in version 1.1.21:

The regularized log transformation uses the fitted dispersions instead of the MAP dispersions. This prevents large, true log fold changes from being moderated due to a large dispersion estimate blind to the design formula. This behavior is also more consistent with the variance stabilizing transformation.

DEXSeq

Changes in version 2013-09-12:

Major changes to vignette to provide more of an end-to-end description of the work flow.
Major changes to function names to now make TRT rather than BM the default; changed vignette to reflect this.
Added apepndix explaining TRT to vignette.

Changes in version 2013-02-27:

A parameter -r was added to the python scripts, that allow the users either to ignore the exonic bins belonging to several genes and treat the genes separately, or merge the genes into an aggregate gene. The equivalent R implementations of the python scripts were finally added.

Changes in version 2012-11-28:

The TRT method is implemented, for people with a big number of samples without completions or speed issues

Changes in version 2012-06-26:

Now any function relies on the order of the levels of the factors.

Changes in version 2012-05-21:

More options and flexibilty added to “estimatelog2FoldChanges”

Changes in version 2011-10-03:

Changes to the documentation and to the vignette. New functions added and more support for gene names and strange exonids.

Changes in version 2011-07-12:

Parallelization possibility added to the code, with its description in the vignette and single exon genes ignored properly.

Changes in version 2011-07-01:

‘estimateSizeFactors’ and ‘estimatedispersions’ function added as S4 methods, no more problems when loading DESeq and DEXSeq in the same R session

DiffBind

Changes in version 1.8.0:

Add support for DESeq2:
- New: Add DBA_DESEQ2, DBA_ALL_METHODS and DBA_ALL_BLOCK method constants
- Change: dba.analyze can analyze using DESeq2
- Change: all reporting and plotting functions support DESeq2 results
- Change: vignette includes comparison of edgeR, DESeq, and DESeq2
Changes to counting using dba.count:
- Change: optimize built-in counting code to use much less memory and run faster
- Change: deprecate bLowMem, replaced with bUseSummarizeOverlaps
- New: add readFormat parameter to specify read file type (instead of using file suffix)
New: generation of result-based DBA object using dba.report (makes it easier to work with differentially bound peaksets)
Changes to defaults:
- Change: default score is now DBA_SCORE_TMM_MINUS_FULL instead of DBA_SCORE_TMM_MINUS_EFFECTIVE in dba.count
- Change: default value for bFullLibrarySize is now TRUE in dba.analyze
- New: add bCorPlot option to DBA$config to turn off CorPlot by default
Various bugfixes, improved warnings, updated documentation

DOSE

Changes in version 1.99.6:

bug fixed in EXTID2NAME. <2013-09-28, Sat>

Changes in version 1.99.5:

fixed in calculating M when only one categroy presented, the object was matrix insted of list. <2013-09-16, Mon>

Changes in version 1.99.4:

export gsea function <2013-07-10, Wed>

Changes in version 1.99.3:

extend EXTID2NAME to support 20 species <2013-07-09, Tue>
update vignette. <2013-07-09, Tue>

Changes in version 1.99.1:

convert vignette file to knitr Sweave. <2013-06-24, Mon>

Changes in version 1.99.0:

extent ggplot to support enrichResult by implementing fortify method. <2013-05-22, Wed>
re-implement barplot.enrichResult. <2013-05-23, Thu>
enrich.internal support user specifiy background by parameter universe. <2013-05-24, Fri>
implement Gene Set Enrichment Analysis algorithm. <2013-05-29, Wed>
change setReadable to support groupGO of clusterProfiler. <2013-05-29, Wed>
fixed mclapply not support Windows platform issue. <2013-05-30, Fri>
rename logFC parameter to foldChange. <2013-06-13, Thu>

Changes in version 1.7.1:

use geom_bar(stat=”identity”) instead of geom_bar() in barplot for explicitly mapping y value. <2013-05-08, Wed>
bug fixed when qvalue can’t calculated. <2013-05-02, Thu>
bug fixed of enrich.internal, drop those genes that without annotation when calculating sample gene number. <2013-05-02, Thu>
change some code to satisfy ReactomePA <2013-03-27, Wed>

DSS

Changes in version 1.7.0:

Added functionalities for multiple factor experimental design. Currently edgeR functions are used for glm fitting and hypothesis testing. DSS only provide functions for dispersion estimation.

Changes in version 1.6.0:

Implemented methods for detecting differentially methylated loci (DML).

EBImage

Changes in version 4.4.0:

NEW FEATURES

New colorLabels function color-coding labels of object masks by a random permutation (Bernd Fisher)
Additional argument inputRange to normalize allowing presetting a limited input intensity range
Additional argument thick to paintObjects controlling the thickness of boundary contours

SIGNIFICANT USER-VISIBLE CHANGES

normalize and combine use the generics from BiocGenerics
removed the along argument from combine
Re-introduced calculation of ‘s.radius.sd’ (standard deviation of the mean radius) in cell features

BUG FIXES

getFrame: XY dimensions equal 1 were dropped

edgeR

Changes in version 3.3.8:

predFC() with design=NULL now uses normalization factors correctly. However this use of predFC() to compute counts per million is being phased out in favour of cpm().

Changes in version 3.3.5:

Refinement to cutWithMinN() to make the bin numbers more equal in the worst case.
estimateDisp() now creates the design matrix correctly when the design matrix is not given as an argument and there is only one group. Previously this case gave an error.
Minor edit to glm.h code.

Changes in version 3.3.4:

plotMDS.DGEList now gives a friendly error message when there are fewer than 3 data columns.

Changes in version 3.3.3:

DGEList() accepts NULL as a possible value again for the group, lib.size and norm.factors arguments. It is treated the same way as a missing argument.

Changes in version 3.3.2:

Update to cutWithMinN() so that it does not fail even when there are many repeated x values.
Refinement to computation for nbins in dispBinTrend. Now changes more smoothly with the number of genes. trace argument is retired.
Fixes to calcNormFactors with method=”TMM” so that it takes account of lib.size and refCol if these are preset.
Updates to help pages for the data classes.

Changes in version 3.3.1:

Updates to DGEList() and DGEList-class documentation. Arguments lib.size, group and norm.factors are now set to their defaults in the function definition rather than set to NULL.

eiR

Changes in version 1.2.0:

NEW FEATURES

speed improvements

NEW FEATURES

ieInit now accepts a SNOW cluster for parallel inserts

NEW FEATURES

allow compounds to be updated in-place by name

NEW FEATURES

eiQuery can now return similarity values instead of distances

fabia

Changes in version 2.6.1:

NEW FEATURES

rescaling of lapla

NEW FEATURES

extractPlot does not plot sorted matrices

FGNet

Changes in version 1.0.0:

NEW FEATURES

Package released

flowType

Changes in version 2.0.0:

NEW FEATURES

New flowType using an enhanced dynamic programming algorithm implemented in C++, allowing for searching only a subset of the phenotype space (to make very high-dimensional data like CyTOF and single cell RT-PCR feasible), and to allow the setting of multiple levels of expression.

NEW FEATURES

Note: this version brings some minor but necessary changes to the way in which the flowType function is called, which may break backwards compatibility for some users. Also note that the return value from flowType is no longer compatible with version 1.x of RchyOptimyx; users wishing to use RchyOptimyx with flowType 2.x should use the new and improved version 2.x of RchyOptimyx, which is actually simpler and much more intuitive.

fmcsR

Changes in version 1.4.0:

NEW FEATURES

Package and fmcsR algorithm published in Bioinformatics (Sep 4, 2013, Epub ahead of print)

NEW FEATURES

fmcsR outperforms most other virtual screening (VP) methods

gage

Changes in version 2.11.3:

add secondary vignette, “RNA-Seq Data Pathway and Gene-set Analysis Workflows”.
add function kegg.gsets, which generates up-to-date KEGG pathway gene sets for any specified KEGG species.

gCMAP

Changes in version 1.5.4:

NEW: The bigmemory and bigmemoryExtras packages are not optional, enabling use of gCMAP on Windows

Changes in version 1.5.3:

NEW: Updated titles of vignettes

Changes in version 1.5.2:

BUGFIX: Updated eSet construction in mapNmerge function

Changes in version 1.5.1:

BUGFIX: fixed incorrect varMetaData element definition in .process_counts

gCMAPWeb

Changes in version 1.1.7:

BUGFIXFixed memory leak and enabled html_table function to deal with multibyte strings.

Changes in version 1.1.6:

UPDATEgCMAPWeb now issues an error when javascript is not available in the browser.

Changes in version 1.1.2:

NEW: Added tutorial as a new vignette.

Changes in version 1.1.1:

BUGFIX: Heatmaps are now displayed for results of directional query.

geNetClassifier

Changes in version 1.1.1:

BUG FIXES

plotDiscriminantPower now accepts feature names starting by number (i.e. affy probes)

GeneticsPed

Changes in version 2007-09-12:

Added prune function for pruning/trimming the pedigree. It does not work on pedigree, but assumes a data.frame with defined structure. Adaption needed.
We depend on genetics package since gpLong2Wide and hwp assume that input is of genotype class.
Added two utility functions (gpLong2Wide and hwp) for work with gpi(). There is also a separate help page for them.
Internal fixes in gpi - no need to transpose inputs for Fortran call anymore - check that there are no NA values in gp and hwp

Changes in version 2007-04-25:

Version bump to follow BioC releases. # 0.1.4

Changes in version 2007-04-19:

Added internal .get* functions for retrieving slot values and use of it.

Changes in version 2007-04-18:

R CMD check should now fail also when R error (usually call to stop()) occurs in unit testing.
Added unit tests for sort, examples in help page and clarified sort help page.

Changes in version 2007-04-06:

New small dataset Falconer5.1.
Added sex(), sex<-(), ascendantSex() and ascendantSex<-() functions.
Added some more tests for relationshipAdditive, inverseAdditive and inbreeding. # 0.1.2

Changes in version 2007-04-01:

Now we are more rigorous for value of ascendantSex argument in Pedigree(). It must accord to values in sex column, if that one is passed of course.
MASS added to depends due to use of fractions() in many places in documnetation.
Added vignette on quantitative genetic (animal) model and model.matrix.Pedigree() functions for educational purposes.
Created data directory and added pedigree example Mrode2.1 and Mrode3.1.
Added unit tests for genetic relationship matrices that should test all related functions - mainly against Mrode’s book examples - runit.genRelMatrix.R.
Added arguments sort and names to inverseAdditive(), relationshipAdditive() and inbreeding().
Reworked core for relationshipAdditive() into vectorized form.
Added geneFlowT(), geneFlowTinv(), geneFlowM() and mendelianSamplingD() functions.

Changes in version 2007-04:

Implemented sort by pedigree information only. # 0.1.3

Changes in version 2007-03-02:

Registration of native routines - src/register.cc.
Added gpi() function. # 0.1.1
Temporarily removed unknown funcs, due to planned move to BioC and change to S4.
All depends are now in gdata –> removing ggmisc.

Changes in version 2006-03-29:

codeUnit to get internal codes for subject and ascendants if factors are used.
Handled unused levels in nlevels.pedigree and summary.pedigree now produces a simple summary
Started to implement checks in check.pedigree and friends
Proper factor handling

Changes in version 2006-03-16:

Playing around with NA/unknown representation - it is very likely that I messed up some things with factors –> subject to changes. # Version 0.1
Initial version # NEWS ends here

GenomicFeatures

Changes in version 1.14:

NEW FEATURES

keys method now has new arguments to allow for more sophisticated filtering.
adds genes() extractor
makeTranscriptDbFromGFF() now handles even more different kinds of GFF files.

BUG FIXES

better argument checking for makeTranscriptDbFromGFF()
cols arguments and methods will now be columns arguments and methods

GenomicRanges

Changes in version 1.14.0:

NEW FEATURES

Add coercion from GenomicRangesList to RangedDataList.
Add “c” method for GAlignmentsPairs objects.
Add coercion from GAlignmentPairs to GAlignmentsList.
Add ‘inter.feature’ and ‘fragment’ arguments to summarizeOverlaps().
Add seqselect,GAlignments-method.
Add CIGAR utilities: explodeCigarOps(), explodeCigarOpLengths() cigarRangesAlongReferenceSpace(), cigarRangesAlongQuerySpace() cigarRangesAlongPairwiseSpace(), extractAlignmentRangesOnReference() cigarWidthAlongReferenceSpace(), cigarWidthAlongQuerySpace() cigarWidthAlongPairwiseSpace().
Add seqlevels0() and restoreSeqlevels().
Add seqlevelsInUse() getter for GRanges, GRangesList, GAlignments GAlignmentPairs, GAlignmentsList and SummarizedExperiment objects.
Add update,GAlignments method.
Add GIntervalTree class.
Add coercion from GAlignmentPairs to GAlignments.
Add sortSeqlevels().
Add tileGenome().
Add makeGRangesFromDataFrame() and coercion from data.frame or DataFrame to GRanges.

SIGNIFICANT USER-LEVEL CHANGES

Renaming (with aliases from old to new names): - classes GappedAlignments -> GAlignments GappedAlignmentPairs -> GAlignmentPairs - functions GappedAlignments() -> GAlignments() GappedAlignmentPairs() -> GAlignmentPairs() readGappedAlignments() -> readGAlignments() readGappedAlignmentPairs() -> readGAlignmentPairs()
Remove ‘asProperPairs’ argument to readGAlignmentsList().
Modify “show” method for Seqinfo object to honor showHeadLines and showTailLines global options.
50x speedup or more when merging 2 Seqinfo objects, 1 very small and 1 very big.
Add dependency on new XVector package.
Enhanced examples for renaming seqlevels in seqlevels-utils.Rd.
More efficient reference class constructor for ‘assays’ slot of SummarizedExperiment objects.
‘colData’ slot of SummarizedExperiment produced from call to summarizedOverlaps() now holds the class type and length of ‘reads’.
4x speedup to cigarToRleList().
Relax SummarizedExperiment class validity.
Renaming (with aliases from old to new names): cigarToWidth() -> cigarWidthOnReferenceSpace(), and cigarToQWidth() -> cigarWidthOnQuerySpace().
Improvements to summarizeOverlaps(): - mode ‘Union’: 1.5x to 2x speedup - mode ‘IntersectionNotEmpty’: 2x to 8x speedup + memory footprint reduced by ~ half
Change default ‘use.names’ to FALSE for readGAlignmentsList().
Implement ‘type=”equal”’ for findOverlaps,SummarizedExperiment methods.
Modify summarizeOverlaps() examples to use ‘asMates=TRUE’ instead of ‘obeyQname=TRUE’.
Remove unneeded “window” method for GenomicRanges objects.
Speed up seqinfo() getter and setter on SummarizedExperiment objects and derivatives (e.g. VCF) by using direct access to ‘rowData’ slot.
coverage,GenomicRanges method now uses .Ranges.coverage() when using the defaults for ‘shift’ and ‘width’.
Remove restriction that metadata column names must be different on a GRangesList and the unlisted GRanges.
GenomicRangesUseCases vignette has been redone and renamed to GenomicRangesHOWTOs

DEPRECATED AND DEFUNCT

Defunct all “match” and “%in%” methods in the package except for those with the GenomicRanges,GenomicRanges signature.
Deprecate GappedAlignment*: - GappedAlignments and GappedAlignmentPairs classes - GappedAlignments() and GappedAlignmentPairs() constructors - readGappedAlignments() and readGappedAlignmentPairs() functions
Deprecate cigar util functions: cigarToWidth(), cigarToQWidth(), cigarToIRanges() splitCigar(), cigarToIRanges(), cigarToIRangesListByAlignment() cigarToIRangesListByRName(), cigarToWidth(), cigarToQWidth() cigarToCigarTable(), summarizeCigarTable()
Deprecate seqselect().

BUG FIXES

Fix bug in c,GAlignments for case when objects were unnamed.
Fix bug in flank,GenomicRanges (when ‘ignore.strand=TRUE’ ‘start’ was being set to TRUE).
Fix bug in behavior of summarizeOverlaps() count mode ‘IntersectionNotEmpty’ when ‘inter.features=FALSE’. Shared regions are now removed before counting.
Fix bug in cigarToIRangesListByAlignment() when ‘flag’ is supplied and indicates some reads are unmapped.
Fix bug in summarizeOverlaps(…, mode=’IntersectionNotEmpty’) when ‘features’ has ‘-‘ and ‘+’ elements and ‘ignore.strand=TRUE’.
match,GenomicRanges,GenomicRanges method now handles properly objects with seqlevels not in the same order.

GGtools

Changes in version 4.10:

Sharply revised vignette

Changes in version 4.9:

All.cis accepts a CisConfig instance to define parameters of a cis search

gmapR

Changes in version 1.4.0:

NEW FEATURES

Add desired_read_group to BamTallyParam; will limit tallies to that specific read group (useful for multi-amplicon sequencing, like Fluidigm)
Add keep_ref_rows argument to variantSummary() for keeping rows for positions where no alt is detected (the rows where ref == alt).
gsnap() will now output a GsnapOutputList when there are multiple input files
Support ‘terminal_threshold’ and ‘gmap_mode’ parameters in GsnapParam, and use different defaults for DNA vs. RNA. This means a big improvement in alignment quality for DNA.
GmapGenome now accepts a direct path to the genome as its first argument

USER-VISIBLE CHANGES

Renamed summarizeVariants to variantSummary
The ‘which’ in GsnapParam is now a GenomicRanges instead of a RangesList
Refactor bam_tally, so that bam_tally returns a TallyIIT object, which is then summarized via summarizeVariants; this allows computing tallies once and summarizing them in different ways (like maybe get the coverage). The summarizeVariants function yields a VRanges.

BUG FIXES

fix minimum quality cutoff check to >=, instead of >
fix asBam,GsnapOutput for when unique_only is TRUE
package created by makeGmapGenomePackage now have a GmapGenome with the correct name

GOSemSim

Changes in version 1.19.3:

add getSupported_Org function for accessing all the names of supported organisms <2013-07-09, Mon>

Changes in version 1.19.2:

export getDb and loadGOMap <2013-07-09, Mon>
update vignettes <2013-07-9, Mon>

Changes in version 1.19.1:

update vignettes <2013-06-13, Thu>

GSEABase

Changes in version 1.23:

SIGNIFICANT USER-VISIBLE CHANGES

Support ‘c7’ broad set

SIGNIFICANT USER-VISIBLE CHANGES

Warn or remove duplicate geneIds when parsing GMT or Broad XML

GWASTools

Changes in version 1.7.8:

Added gdsSetMissingGenotypes, updated argument names in ncdfSetMissingGenotypes.
Changed colorscheme in manhattanPlot.R.
Bug fix in ibdPlot - diagonal orange bars are back.
Bug fix in plinkWrite for writing just one sample.
Bug fix in printing pedigreeCheck error message.

Changes in version 1.7.7:

Changed handling of GxE interaction variables in assocTestRegression.

Changes in version 1.7.6:

Updated vignette for SNPRelate 0.9.16.

Changes in version 1.7.5:

gwasExactHW will run on all chromosomes except (Y,M), rather than (autosome,X,XY) only.

Changes in version 1.7.4:

More informative error messages in anomDetectBAF and anomDetectLOH.

Changes in version 1.7.3:

Changed labeling of IBD plots from “HS” to “Deg2” and “FC” to “Deg3.”
Bug fix in pedigreePairwiseRelatedness - no more warning about multiple values passed to stringsAsFactor.
pedigreeClean and pedigreeFindDuplicates are now defunct. Use pedigreeCheck instead.

hapFabia

Changes in version 1.2.2:

bug fix split_sparse_matrix
plot functions with other arguments ‘…’
plot arguments grid and pairs
new function ‘plotLarger’ (add samples without IBD and borders)
vcftoFABIA with command line options -s (SNVs_) and -o (output file)
vcftoFABIA in R with output file name

HiTC

Changes in version 1.5.2:

NEW FEATURES

Efficient memory matrix representation using the Matrix package. The memory usage for big sparse matrix is improved by a factor 7. However, some operation are much slower based on the Matrix implementation. Thus, for some task as the plotting function, the Matrix are converted in standard matrix based object
‘show’ and ‘detail’ method for HTClist object
‘c(x, …)’ method for HTCexp and HTClist objects

SIGNIFICANT USER-VISIBLE CHANGES

The option mask.data from the mapC function is deprecated
Update of parallel computation for some functions (import, normalize)

BUG FIXES

Bug Fixe in import.my5C for ChrM

Changes in version 1.5.1:

BUG FIXES

Fix bug in HTCexp contructor for matrix of dim 1

BUG FIXES

Fix bug in import.my5C for matrix of dim 1

BUG FIXES

Fix bug for title display on HTCexp plots

BUG FIXES

Fix bug in HiTClist plot due to chromosome order

BUG FIXES

Correct errors in the man pages

hpar

Changes in version 1.3.1:

Updated to HPA version 11 <2013-04-11 Thu>

Changes in version 1.3.0:

Bioc 2.13 devel version bump

HTSeqGenie

Changes in version 3.11.10:

vignette updated to build on BioC dev

Changes in version 3.11.9:

TP53GenomicFeatures() now uses the same temp dir as TP53Genome(), to fix a build issues on BioC servers

Changes in version 3.11.8:

-choice of VT filters configurable via config

Changes in version 3.11.7:

mergeBams(…, sort=FALSE) in alignReads.R: since bams are already sorted in chunks, merging preserves the order and no re-sorting should is necessary

Changes in version 3.11.6:

saveCoverage now outputs a summary.coverage summary file

Changes in version 3.11.5:

directly export coverage from Rle with rtracklayer::export (instead of to make a memory-costly convertsion to a RangedData object)

Changes in version 3.11.4:

update variant calling code to work with VariantTools 1.3.6
include Jens’ minlength=1 modification to handle reads fully trimmed

Changes in version 3.11.3:

exports loginfo, logdebug, logwarn, logerror
uses TallyVariantsParam and as(,”VRanges”) to fix a bug preventing compilation on BioC
the number of threads used during processChunks is divided by 2 due to an erroneous extra mcparallel(…) step in sclapply/safeExecute
use a maximum of 12 cores in preprocessReads

Changes in version 3.11.2:

trim lowest quality tail of reads according to Illumina manual. This new quality step precedes the regular quality filtering that is still done.

Changes in version 3.11.1:

allow to use better filters for variant tools by default, uses standard filters (bad), but if repeat masked track and dbsnp are given in config it uses those.

Changes in version 3.11.0:

starting the new development branch

Changes in version 3.10.1:

release version

htSeqTools

Changes in version 1.7.1:

Added findPeakHeight function to estimate optimal minHeight value based on False Discovery Rate for using in enrichedPeaks

HTSFilter

Changes in version 1.0.1:

– Updated citation information, minor updates to vignette – DESeq2, IRanges, and GenomicRanges added to Imports field, and HTSFilter and HTSFilterBasic methods written for objects of with DESeqDataSet signature (from DESeq2 pipeline). Examples illustrating the use of HTSFilter have also been added in the documentation and vignettes. – DESeq and edgeR moved to Imports field (thanks to Denis Laloë for the suggestion) – Warning message added when gene ID’s are included as a column in the data frame (thanks to Luc Jouneau for the suggestion)

hyperdraw

Changes in version 1.13.1:

Node labels were ignoring the ‘cex’ node data value (reported by Hannes Hettling)
Added “start” and “both” options for “arrowLoc” graph attribute (which will draw arrowhead at both ends of hyper edges)
Bug fix for converting Hypergraph to graphBPH so that hyperedge names are used as edge labels (reported by Hannes Hettling)
Update the R version check in drawEdge() to cope properly with major versions greater than 2 (!)

illuminaio

Changes in version 0.3.9:

Added vignette giving examples of usage and demonstrating comparison with GenomeStudio output

Changes in version 0.3.8:

Bug fixes, renaming of readIDAT_bin to readIDAT_nonenc.

Changes in version 0.3.6:

Added one parent function readIDAT which checks file format and dispatches to the relevant subfunction.

Changes in version 0.3.5 (2013-08-02):

Cleaned up internal code of readBPM().
ROBUSTNESS: Added unit tests for readBPM(). Note that these are only run if environment variable ‘R_CHECK_FULL’ is set, i.e. they will not be perfomed on the Bioconductor servers.

imageHTS

Changes in version 1.12.0:

NEW FEATURES

Additional arguments to highlightSegmentation controlling the color (col) and opacity (opac) of nuclei and cell contours, closing of contours at borders (border), and whether highligting of grayscale images should be done in color (toRGB).

SIGNIFICANT USER-VISIBLE CHANGES

removed elongation of the nuclei mask along image borders in segmentATH

intansv

Changes in version 0.99.3:

Notes

Improvement of the vigenette to make it more comprehensive.

Notes

Removal of useless example dataset.

iPAC

Changes in version 1.5.2:

Updated file to be consistent with Bioconductor version numbering. Also fixed a rare bug that gave an error if every residue aligned between mutational and positional data.

IPPD

09-29-2010:

01-12-2011:

01-17-2012:

IRanges

Changes in version 1.20.0:

NEW FEATURES

Add IntervalForest class from Hector Corrada Bravo.
Add a FilterMatrix class, for holding the results of multiple filters.
Add selfmatch() as a faster equivalent of ‘match(x, x)’.
Add “c” method for Views objects (only combine objects with same subject).
Add coercion from SimpleRangesList to SimpleIRangesList.
Add an %outside% that is the opposite of %over%.
Add validation of length() and names() of Vector objects.
Add “duplicated” and “table” methods for Vector objects.
Add some split methods that dispatch to splitAsList() even when only ‘f’ is a Vector.

SIGNIFICANT USER-VISIBLE CHANGES

All functionalities related to XVector objects have been moved to the new XVector package.
Refine how isDisjoint() handles empty ranges.
Remove ‘keepLength’ argument from “window<-“ methods.
unlist( , use.names=FALSE) on a CompressedSplitDataFrameList object now preserves the rownames of the list elements, which is more consistent with what unlist() does on other CompressedList objects.
Splitting a list by a Vector just yields a list, not a List.
The rbind,DataFrame method now handles the case where Rle and vector columns need to be combined (assuming an equivalence between Rle and vector). Also the way the result DataFrame is constructed was changed (avoids undesirable coercions and should be faster).
as.data.frame.DataFrame now passes ‘stringsAsFactors=FALSE’ and ‘check.names=!optional’ to the underlying data.frame() call. as(x,”DataFrame”) sets ‘optional=TRUE’ when delegating. Most places where we called as.data.frame(), we now call ‘as(x,”data.frame”)’.
The [<-,DataFrame method now coerces column sub-replacement value to class of column when the column already exists.
DataFrame() now automatically derives rownames (from the first argument that has some). This is a fairly significant change in behavior, but it probably does better match user behavior.
Make sure that SimpleList objects are coerced to a DataFrame with a single column. The automatic coecion methods created by the methods package were trying to create a DataFrame with one column per element, because DataFrame extends SimpleList.
Change default to ‘compress=TRUE’ for RleList() constructor.
tapply() now handles the case where only INDEX is a Vector (e.g. an Rle object).
Speedup coverage() in the “tiling case” (i.e. when ‘x’ is a tiling of the [1, width] interval). This makes it much faster to turn into an Rle a coverage loaded from a BigWig, WIG or BED as a GRanges object.
Allow logical Rle return values from filter rules.
FilterRules no longer requires its elements to be named.
The select,Vector method now returns a DataFrame even when a single column is selected.
Move is.unsorted() generic to BiocGenerics.

DEPRECATED AND DEFUNCT

Deprecate seqselect() and subsetByRanges().
Deprecate ‘match.if.overlap’ arg of “match” method for Ranges objects.
“match” and “%in%” methods that operate on Views, ViewsList, RangesList, or RangedData objects (20 methods in total) are now defunct.
Remove previously defunct tofactor().

BUG FIXES

The subsetting code for Vector derivatives was substancially refactored. As a consequence, it’s now cleaner, simpler, and [ and [[ behave more consistently across Vector derivatives. Some obscure long-standing bugs have been eliminated and the code can be slightly faster in some circumstances.
Fix bug in findOverlaps(); zero-width ranges in the query no longer produce hits ever (regardless of ‘maxgap’ and ‘minoverlap’ values).
Correctly free memory allocated for linked list of results compiled for findOverlap(select=”all”).
Various fixes for AsIs and DataFrames.
Allow zero-row replacement values in [<-,DataFrame.
Fix long standing segfault in “[” method for Rle objects (when doing Rle()[0]).
“show” methods now display its most specific class when a column or slot is an S3 object for which class() returns more than one class.
“show” methods now display properly cells that are arrays.
Fix the [<-,DataFrame method for when a value DataFrame has matrix columns.
Fix ifelse() for when one or more of the arguments are Rle objects.
Fix coercion from SimpleList to CompressedList via AtomicList constructors.
Make “show” methods robust to “showHeadLines” and “showTailLines” global options set to NA, Inf or non-integer values.
Fix error condition in eval,FilterRules method.
Corrected an error formatting in eval,FilterRules,ANY method.

isobar

Changes in version 1.7.6:

added TMT 10plex (contribution from Florent Gluck)
fixed bugs with system.file not working on R < 2.11 (contribution from Florent Gluck)
fixed bug in isobar-qc which was not working without normalize=TRUE
added writeHscoreData for usage with Hscorer.py (MM Savitski, 2010)
shQuote commands correctly - should fix issues running report generation on Windows
added calculations and XLS tab for peptides with unsure localization of the modification site
updated scripts for creating multi-sample reports (create.meta.reports)

Changes in version 1.7.5:

fixed critical bugs: Excel report output had wrong ordering, ie ratios did not correspond to the meta information [introduced in version 1.7.3].
fix of real peptide names: Reexport I/L peptides in reports

Changes in version 1.7.4:

improved MSGF+ search result import
refactored report properties: all properties can now be defined in in the properties.R
speed and memory usage improvements when creating wide XLS report
ratio p-value adjustment now works per comparision instead of globally

Changes in version 1.7.3:

fix wide XLS report format
novel plot for ratio combinations in QC report showing individual ratio distributions and significant ratios

Changes in version 1.7.2:

added TMT 6plex masses to phosphoRS export script
fixed mascot parsers
MzIdentML version 1.1.0 support implemented [not fully tested]

Changes in version 1.7.1:

fixed import of MzIdentML files from Mascot and ProteomeDiscoverer

KEGGgraph

KEGGprofile

lmdme

Changes in version 1.3.1:

BUGS FIXED

NA manipulation of lmFit for coefficient is now contemplated

Changes in version 1.3.0:

MINOR CHANGES

Bump y in version x.y.z to odd number in devel

MANOR

Changes in version 2013-07-03 (2013-07-03):

Replaced calls to ‘exit’, ‘fprintf’ which now raise a WARNING upon check.
Iteration index not printed anymore in ‘nem’ (raised an error when compiling the vignette).

Changes in version 2011-03-18 (2011-03-18):

Updated calls to ‘GLAD:::daglad’ in the vignette to fix an error caused by changes in the defaults of ‘daglad’.

Changes in version 2010-10-01 (2010-10-01):

Cleaned ‘data/flags.RData” which contained objects from an old ‘globalenv’.
Updated maintainer’s email address.

Changes in version 2010-01-24 (2010-01-24):

Added (back) ‘intensity.flag’ to ‘data/flags.RData’ (had been removed since v 1.12.0 for an unknown reason).

Changes in version 2009-01-15 (2009-01-15):

misplaced alignment tab in man/spatial.Rd.

Changes in version 2009-01-13 (2009-01-13):

updated references in .Rd files.
fixed warnings due to incorrect use of \item in .Rd files.

Changes in version 2009-01-06 (2009-01-06):

‘norm’ and ‘sort’ are now S3 methods as well

Changes in version 2009-01-04 (2009-01-04):

(almost) one file per function in R/
removed empty section \details in man/qscore.Rd
added a NAMESPACE
removed inst/doc/Makefile (not needed anymore because no html output required)

Changes in version 2009-01-02 (2009-01-02):

removed another non-standard keyword

Changes in version 2009-01-01 (2009-01-01):

only one keyword per \keyword entry…

Changes in version 2008-12-31 (2008-12-31):

now use standard “keyword”s
changed \link{\code{stuff}} into \code{\link{stuff}}

Changes in version 2008-11-26 (2008-11-26):

filled in “keyword” sections in .Rd files.
removed empty “examples” sections from .Rd files.
initialized a few variables upon declaration in C code to prevent warnings in R CMD CHECK.

Changes in version 2008-09-23 (2008-09-23):

modification de la fonction cv pour retourner NA lorsque toutes la valeurs du vecteur sont <e0> NA
modification de la function getChromosomeArm pour que cytoband ne soit pas positionn<e9>e <e0> NULL

Changes in version 2008-09-04 (2008-09-04):

added a CHANGELOG
updated outdated reference in the .bib file
changed the definition of flag “rep.flag” to avoid the error now caused by sd(NA, na.rm=TRUE)

metagenomeSeq

Changes in version 1.2 (2013-08-20):

Our paper got accepted and is available!
Added methods for MRexperiment objects (colSums,colMeans,rowSums,rowMeans, usage is for example colSums(obj) or colSums(obj,norm=TRUE)) (09-25)
Added two new functions, plotOrd and plotRare - a function to plot PCA/MDS coordinates and rarefaction effect (09-04,09-18)
Updated MRfisher to include thresholding for presence-absence testing (08-19)
Updated comments (roxygen2) style for all the functions using the Rd2roxygen package (07-13)
Updated plotCorr and plotMRheatmap to allow various colors/not require trials(07-13)
Rewrote vignette (and switched to knitr)

Changes in version 1.1 (2013-06-25):

Rewrote load_meta and load_metaQ to be faster/use less memory
Modified cumNormStat to remove NA samples from calculations (example would be samples without any counts)
Re-added plotGenus’ jitter
Fixed uniqueNames call in the MR tables
Changed thanks to Kasper Daniel Hansen’s suggestions the following: plotOTU and plotGenus both have much better auto-generated axis MRtable, MRfulltable, MRcoefs have a sort by p-value option now MRtable, MRfulltable, MRcoefs now have an extra option to include unique numbers for OTU features (default would automatically add them previously) cumNorm.R - now returns the object as well - not just replacing the environment 0 Still need to turn the fitZig output to S3, consider subsetting function address low p-values

minfi

Changes in version 1.7:

Added getMethSignal(), a convenience function for programming.
Changed the argument name of “type” to “what” for getMethSignal().
Added the class “RatioSet”, like “GenomicRatioSet” but without the genome information.
Bugfixes to the “GenomicRatioSet()” constructor.
Added the method ratioConvert(), for converting a “MethylSet” to a “RatioSet” or a “GenomicMethylSet” to a “GenomicRatioSet”.
Fixed an issue with GenomicMethylSet() and GenomicRatioSet() caused by a recent change to a non-exported function in the GenomicRanges package (Reported by Gustavo Fernandez Bayon gbayon@gmail.com).
Added fixMethOutliers for thresholding extreme observations in the [un]methylation channels.
Added getSex, addSex, plotSex for estimating sex of the samples.
Added getQC, addQC, plotQC for a very simple quality control measure.
Added minfiQC for a one-stop function for quality control measures.
Changed some verbose=TRUE output in various functions.
Added preprocessQuantile.
Added bumphunter method for “GenomicRatioSet”.
Handling signed zero in minfi:::.digestMatrix which caused unit tests to fail on Windows.
addSex and addQC lead to sampleNames() being dropped because of a likely bug in cbind(DataFrame, DataFrame). Work-around has been implemented.
Re-ran the test data generator.
Fixed some Depends and Imports issues revealed by new features of R CMD check.
Added blockFinder and cpgCollapse.
(internal) added convenience functions for argument checking.
Exposed and re-wrote getAnnotation().
Changed getLocations() from being a method to a simple function. Arguments have been removed (for example, now the function always drops non-mapping loci).
Implemented getIslandStatus(), getProbeType(), getSnpInfo() and addSnpInfo(). The two later functions retrieve pre-computed SNP overlaps, and the new annotation object includes SNPs based on dbSNP 137, 135 and 132.
Changed the IlluminaMethylatioAnnotation class to now include genomeBuild information as well as defaults.
Added estimateCellCounts for deconvolution of cell types in whole blood. Thanks to Andrew Jaffe and Andres Houseman.

mitoODE

Changes in version 0.99.6:

changed mc.cores to 1 to avoid Windows building error

Changes in version 0.99.5:

changed mc.cores=12 by mc.cores=detectCores()

Changes in version 0.99.2:

initial submission

motifStack

Changes in version 1.5.4:

NEW FEATURES

use BiocStyle to write vignette

BUG FIXES

No changes classified as ‘bug fixes’ (package under active development)

Changes in version 1.5.3:

NEW FEATURES

No changes classified as ‘new features’ (package under active development)

BUG FIXES

fix the bug that motifStack can not plot color correctly for radialPhylog layout in motifStack().

Changes in version 1.5.2:

NEW FEATURES

use log-likelihood ratio (ALLR) to do alignment

BUG FIXES

No changes classified as ‘bug fixes’ (package under active development)

Changes in version 1.5.1:

NEW FEATURES

plotMotifStackWithRadialPhylog can draw motif cloud in RadialPhylog style. Check vignette to see the details

BUG FIXES

check mode of pcm and pfm matrix, which should be numeric

MSnbase

Changes in version 1.9.12:

fix MSnSet -> ExpressionSet <2013-10-13 Sun>
MSnSet -> ExpressionSet unit test <2013-10-13 Sun>

Changes in version 1.9.11:

MIAPE to MIAME conversion <2013-10-11 Fri>
proper MIAME when MSnSet -> ExpressionSet <2013-10-11 Fri>

Changes in version 1.9.10:

faster plotMzDelta <2013-09-28 Sat>
faster plotMzDelta for mzRramp instances <2013-09-29 Sun>
chromatogram method <2013-10-04 Fri>
plotMzDelta has subset arg <2013-10-04 Fri>
xic method <2013-10-04 Fri>
suggesting msdata for chromatogram example <2013-10-04 Fri>
renamed plotting arg ‘centroided.’ <2013-10-04 Fri>

Changes in version 1.9.9:

typo in filterNA Rd <2013-09-18 Wed>
writeMgfData now has a progress bar <2013-09-24 Tue>
centroided(MSnExp) <- TRUE now allowed <2013-09-24 Tue>

Changes in version 1.9.8:

using new.env(parent=emptyenv()) to get rid of enclosing env when creating new MSnExps <2013-09-17 Tue>
new (private) MSnExp.size function <2013-09-17 Tue>

Changes in version 1.9.7:

Passing … to read.table in MSnbase:::readIspy[Silac|15N]Data <2013-09-16 Mon>
QualityControl biocView <2013-09-16 Mon>

Changes in version 1.9.6:

new as.data.frame.MSnSet method <2013-08-16 Fri>
new ms2df function <2013-08-16 Fri>
new getEcols and grepEcols helpers for readMSnSet2 <2013-08-16 Fri>

Changes in version 1.9.5:

typo in Author[s]@R <2013-05-15 Wed>

Changes in version 1.9.4:

new simple MSnSet constructor <2013-05-07 Tue>

Changes in version 1.9.3:

Using knitr as VignetteEngine <2013-04-29 Mon>
Remove LazyLoad from DESCRIPTION, which is default nowadays <2013-04-29 Mon>
knitr dependency > 1.1.0 for VignetteBuilder <2013-04-29 Mon>
Adding MSnSet creating sections in io vignette <2013-04-29 Mon>
new readMSnSet2 function <2013-04-30 Tue>

Changes in version 1.9.2:

clean has now a all param (default FALSE is retain original behavious) to remove all 0 intensity values <2013-04-17 Wed>
using BiocGenerics::normalize <2013-04-25 Thu>

Changes in version 1.9.1:

new logging utility function to update an MSnSet’s processingData(object)$processing <2013-03-29 Fri>
Proper logging in t.MSnSet <2013-03-29 Fri>

Changes in version 1.9.0:

new Bioc 2.13 devel version

MSstats

Changes in version 1.99.1:

fixed several NOTES, added .Rbuildignore, compacted vignettes
TODO: check remaining ‘no visible binding for global variable’ NOTES
removed warn -1
added validity check when returning MSnSet
used inherits/is. for class testing
TODO fix if conditions syntax

Changes in version 1.99.0:

improve efficiency for computing groupComparison and quantification <2012-12-21>
add .rnw <2012-12-03>
update groupComparision for label-free time-course experiment with single Feature and with or without technical replicates <2013-04-08>
add option for saving QQ plot and Residual plot in order to checkin the normality assumption in groupComparison function. <2013-04-08>
use ggplot2 package for all plots. <2013-07-11>
fix bug for volcano plot : different color labeling <2013-07-12>
add power plot in sample size calculation plot <2013-07-12>
add ‘interference=TRUE or FALSE’ in sample size calculation <2013-07-15>
add ‘legend.size=7’for size of feature name legends in dataProcessPlots <2013-07-23>
add ‘text.angle=0’for angle of condition labeling in dataProcessPlots <2013-07-23>
fix bug for quantification : when there are missing values in endogenous intensities, but values in reference intensities. <2013-07-24>
fix bug for groupComparison : when there are missing values in endogenous intensities, but values in reference intensities, .make.constast.based or .free sub function were changed. <2013-07-25>
two function for transformation between required input for MSstats and MSnSet class <2013-09-04>
flexibility for visualization : save as pdf files or show in window with selected proteins or all proteins. <2013-09-04>
handle unequal variance for feature in groupComparison function with featureVar=TRUE <2013-09-04>
Add ‘missing.action’ for impute missing values in group comparison stage. <2013-09-20>

mzID

Changes in version 0.3.1:

Comment unused functions <2013-07-05 Fri>
Minor typos in vignette <2013-07-05 Fri>

Changes in version 0.3.0:

NEW FEATURES AND FUNCTIONS

Support for mzIdentML v1.0 (thanks Laurent Gatto)

Changes in version 0.2.1:

NEW FEATURES AND FUNCTIONS

Version counter now in BioConductor style

NEW FEATURES AND FUNCTIONS

Namespace now extracted from file instead of hardcoded in the constructor

NEW FEATURES AND FUNCTIONS

mzID constructor now checks the mzIdentML version before parsing (only 1.1.0 supported atm)

Changes in version 0.1-1:

NEW FEATURES AND FUNCTIONS

Added function flatten to create tabular representation of results

Changes in version 0.0-2:

NEW FEATURES AND FUNCTIONS

The package is now fully documented
created helper functions: countChildren, attrExtract and attrExtractNameValuePair
Added NEWS file
Added README.md file
The parser now succesfully imports all test files on the HUPO mzIdentML page

PERFORMANCE

Improvements in the mzIDpsm constructor makes it ~2-3x faster depending on the file size (thanks to countChildren, attrExtract and attrExtractNameValuePair)

Changes in version 0.0-1:

NEW FEATURES AND FUNCTIONS

First build of the package

NEW FEATURES AND FUNCTIONS

Introduction of the classes: mzID, mzIDdatabase, mzIDevidence, mzIDparameters, mzIDpeptides and mzIDpsm with related constructors

mzR

Changes in version 1.7.4:

version bump for Rcpp 0.10.5 <2013-10-02 Wed>

Changes in version 1.7.3:

Fix a compile error with the clang-3.3 compiler

Changes in version 1.7.2:

updated Rcpp number mismatch warning to include versions <2013-08-01 Thu>

Changes in version 1.7.1:

version bump for Rcpp 0.10.4

NOISeq

Changes in version 2.2.0 (2013-10-14):

New function to generate a Quality Control Report in PDF format including all the exploratory plots.
Plot to evaluate RNA composition bias has been changed.
Some bugs have been fixed.

OSAT

Changes in version 1.8.1:

BUG FIXES

“exlude” arg in the gContainer construction now can be used when whole plates are excluded.

NEW FUNCTION

“exlude<-“ is defined as generic and can be used to exclude wells from an existing container object.

pathview

Changes in version 1.1.7:

Graphviz view can automatic choose different types of legends, either on nodes, edges or both depending on the specific pathways.
Vigette has been reformatted: the “Quick start” section added

Changes in version 1.1.6:

Pathview can plot/integrate/compare multiple states/samples in the same graph. Several functions and data objects are revised: including pathview, keggview.native, keggview.graph, render.kegg.node etc. New section on multiple state data with working exampleshas been added.
Vigette has been reformatted: Data integration section splitted into multiple sub-sections.

Changes in version 1.1.5:

Pathview works with species where default KEGG gene ID is not Entrez Gene. Several functions and data objects are revised: including pathview, node.map, sim.mol.data, kegg.species.code, korg. New section on KEGG species and Gene ID usage with working exampleshas been added.

Changes in version 1.1.3:

Pathview paper published in Bioinformatics

phyloseq

piano

Changes in version 1.2.0:

NEW FEATURES

Added argument ncpus to runGSA(). Enables parts of this function to run in parallel, thus decreasing runtime. Requires R package snowfall.
Added function runGSAhyper() to perform gene set analysis using Fisher’s exact test, as an alternative to runGSA.
Added information about genes in each area of the Venn diagram in the output of diffExp().
Added volcano plot as optional output of diffExp() and added argument volcanoFC.
Added argument ncharLabel to networkPlot() and consensusHeatmap() to control the length of the labels in the plots and add the option to not truncate them.
Added the yeast metabolic model iTO977 to be loaded with loadGSC(), for detecting reporter metabolites using gene set analysis. (See vignette.)
Added support for running networkPlot() on objects returned by runGSAhyper().

USER-VISIBLE CHANGES

Minor updates to the vignette.
Updated diffExp() man page.
Updated the main legend of the plot from consensusScores() to make it clearer.
Updated error-messages in networkPlot().
Fixed typo in PC variance plot produced by runQC().
Restructered this NEWS file.

BUG FIXES

Updated diffExp() to handle changes in lmFit() and topTable() from limma.
Removed suppressWarnings(), as temporarily introduced in version 1.0.1, in polarPlot() around the calls to radial.plot() since warnings are now fixed in package plotrix.

Changes in version 1.0.7:

USER-VISIBLE CHANGES

Updated consensusScores() man page.

Changes in version 1.0.6:

USER-VISIBLE CHANGES

Updated loadMAdata() man page.

Changes in version 1.0.5:

BUG FIXES

Updated diffExp() to only use vennDiagram() of the limma package for Venn diagram plotting in order to correct a bug when plotting more than three circles. Also updated the corresponding man page.

USER-VISIBLE CHANGES

Updated the SBML section in the loadGSC() man page.

Changes in version 1.0.4:

BUG FIXES

Fixed bug in loadMAdata so that also compressed CEL-files (*.CEL.gz) can be loaded correctly.

Changes in version 1.0.3:

USER-VISIBLE CHANGES

Updated references in vignette.

Changes in version 1.0.2:

USER-VISIBLE CHANGES

Updated CITATION information.

Changes in version 1.0.1:

USER-VISIBLE CHANGES

Updated CITATION information.
Fixed typos in DESCRIPTION and piano-package.Rd.
Updated the man file for loadGSC().
Added URL in DESCRIPTION.

BUG FIXES

Fixed bug in loadGSC() so that gmt-files are now loaded correctly.
Temporarily added suppressWarnings() in polarPlot() around the calls to radial.plot() since warnings appeared for example(“radial.plot”) in plotrix v3.4-6.

plethy

Changes in version 0.99.4:

SIGNIFICANT USER-VISIBLE CHANGES

The ‘BuxcoR’ package is now renamed ‘plethy’ as of version 0.99.3.

NEW FEATURES

Added ‘get.labels.by.sample’, ‘get.err.breaks’ and ‘adjust.labels’ to assist with QA/QC of data.

plgem

Changes in version 1.33.1:

minor changes: –removed unnecessary calls to `which’ within subsetting operations, to avoid potential unintended consequences pointed out by Wolfgang Huber: https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004353.html

ProCoNA

Changes in version 0.99.2:

removed a random component in the unit tests that could cause failure.

Changes in version 0.99.1:

Major update … moved to S4 methods (getters, setters, setMethods, etc).
Smaller sample data set for quick example runs in the man pages.
Integration with the MSnbase package. See the vignette for an example of raw data processing in preparation for network building. The main buildProconaNetwork function now takes either matrices of peptide data, or MSnSet objects containing data.
Man pages relating to the main proconaNet object have been combined.

pRoloc

Changes in version 1.1.8:

semi-sup and sup comparison sections in ml vig <2013-10-09 Wed>

Changes in version 1.1.7:

getMarkers has names arg <2013-10-01 Tue>

Changes in version 1.1.6:

new outliers arg to plot2D <2013-09-23 Mon>
cite addMarkers in vignette <2013-09-26 Thu>
add code chunk in poster vig <2013-09-26 Thu>

Changes in version 1.1.5:

added biocViews <2013-09-19 Thu>
added knitr vig engine in ml <2013-09-19 Thu>
import dependencies <2013-09-20 Fri>

Changes in version 1.1.4:

building ml vignette in Makefile <2013-09-11 Wed>

Changes in version 1.1.3:

new private anyUnknown function, used in phenoDisco, to check for the presence of unlabelled (‘unknown’) data <2013-08-27 Tue>
added a note in vignette about “unknown” convention to define protein with unknown localisation <2013-08-28 Wed>
Added HUPO 2011 poster <2013-09-09 Mon>

Changes in version 1.1.2:

fixed Author[s]@R <2013-05-16 Thu>
na.rm=TRUE in f1Count <2013-05-19 Sun>
added CITATION file <2013-06-07 Fri>
new testMarkers function <2013-06-29 Sat>
error message in getBestParams suggests to use testMarkers <2013-06-29 Sat>
nndist methods (see issue #23) <2013-07-01 Mon>
remove unnecessary as.matrix in plot2D’s cmdscale <2013-07-19 Fri>
added plot2D(…, method = “MDS”) example <2013-07-19 Fri>
changed ‘euclidian’ to ‘euclidean’ in nndist_matrix <2013-07-26 Fri>
fixed row ordering in phenoDisco, input and output rownames are now the same <2013-08-13 Tue>
Using filterNA in phenoDisco <2013-08-13 Tue>

Changes in version 1.1.1:

Update README.md to reflect availability in stable release and biocLite installation <2013-04-07 Sun>
new MSe pipeline <2013-04-07 Sun>
perTurbo using Rcpp <2013-04-16 Tue>
initial clustering infrastructure (not exported) <2013-04-17 Wed>
new markerSet function <2013-04-24 Wed>
plsaOptim’s ncomp is now 2:6 <2013-04-27 Sat>
added forword to vignette <2013-04-29 Mon>
default k is now seq(3, 15, 2) in knnOptim <2013-05-09 Thu>

Changes in version 1.1.0:

Bioc 2.13 devel version bump

PWMEnrich

Changes in version 2.4.4:

Vignette update and fix naming of columns in the motif enrichment report

Changes in version 2.4.2:

Improve promoter selection for human and mouse genomes (duplicates are now disregarded)

Changes in version 2.4.0:

Major update with more functions and small bugfixes
Added sequenceReport() and groupReport() for easier report generation
Visualise motif scores along a sequence with plotMotifScores()
Creation of empirical CDFs for motif scores
Almost complete rewrite of the vignette to emphasize the main use cases
Converted documenation to roxygen2

Changes in version 2.3.2:

Subsetting functions for backgrounds from Diego Diez

Changes in version 2.3.1:

Fix a bug with plotTopMotifsSequence() with calling an unknown function
Implement group.only for all background, not only pval in motifEnrichment()
New default to plotMultipleMotifs() so the margins are better

qcmetrics

Changes in version 0.99.3:

fixed template - toc after begin document <2013-10-01 Tue>
updates to vignette <2013-10-01 Tue>
re-reoxygenise rnadeg man <2013-10-01 Tue>

Changes in version 0.99.2:

Implemented Andrzej’s suggestions <2013-09-27 Fri>

Changes in version 0.99.1:

Updated github README file <2013-09-18 Wed>
Added Arnoud’s suggestions to vig <2013-09-21 Sat>
rnadeg wrapper function available in the package <2013-09-21 Sat>
new QcMetadata class <2013-09-21 Sat>
metadata and mdata synonym <2013-09-21 Sat>
added metadata section in knitr reports <2013-09-21 Sat>
selectively import pander::pander.table to fix warning uppon installation <2013-09-21 Sat>
added n15qc wrapper <2013-09-21 Sat>

Changes in version 0.99.0:

submission to Bioconductor <2013-09-17 Tue>

qpgraph

Changes in version 1.18:

USER VISIBLE CHANGES

Updated the formatting of the vignettes to adhere to the Bioconductor style
Functions qpRndHMGM() and qpSampleFromHMGM() which were deprecated in the previous release, are now defunct.

NEW FEATURES

qpCItest() takes now also R/qtl cross objects as input, i.e., the user can test for conditional independence directly on R/qtl cross objects
added functions addGenes(), addeQTL(), and addGeneAssociation() to incrementally build and simulate eQTL networks

BUG FIXES

Real or integer valued levels in discrete variables now prompt an error when they are not positive integers
qpFunctionalCoherence() handles regulatory modules with just one target without giving an error
reQTLcross() can now simulate an initial eQTL model with no genes
fixed plotting for HMgmm objects

QuasR

Changes in version 1.2.0:

NEW FEATURES

new miRNA-seq sample data; vignette has now workflows for ChIP-seq, RNA-seq, smRNA-seq/miRNA-seq, Bis-seq and allele-specific analysis

NEW FEATURES

qMeth can report methylation states for individual molecules (reportLevel=”alignment”)

NEW FEATURES

qCount/qProfile gain argument to ignore spliced reads in counting

Rbowtie

Changes in version 1.1.1:

NEW FEATURES

updated bowtie to version 1.0.0

RchyOptimyx

2.0:

RDAVIDWebService

Changes in version 0.99.1:

MINOR CHANGES

dontrun tags have been removed from plotting examples (Thanks to Valerie Obenchain).

Changes in version 0.99.0:

DOCUMENTATION

NEWS file was added.

ReactomePA

Changes in version 1.5.3:

bug fixed in TERMID2EXTID <2013-09-18, Wed>

Changes in version 1.5.2:

implement gseAnalyzer for GSEA analysis <2013-07-10, Wed>
implement viewPathway for visualizing pathway <2013-07-10, Wed>

Changes in version 1.5.1:

extend enrichPathway to support rat, mouse, celegans, zebrafish, and fly. <2013-03-27, Wed>
modify enrichPathway according to the change of enrich.internal, remove qvalueCutoff parameter, add pAdjustMethod, add universe paramter for user to specify background. <2013-05-29, Wed>

RedeR

Changes in version 2.0.0:

Improved graph attribute settings and interface.

ReportingTools

Changes in version 2013-4-1:

HTML reports are now represented by the HTMLReportRef referenceClass
HTML output now fully customizable via .toHTML, .toDF and .modifyDF arguments to publish (see vignette)
Publication mechanism is abstracted and customizable via ReportHandlers class
ReportingTools output can be used within knitr documents and shiny Web applications (see vignettes knitr.Rmd and shiny.Rnw)
Persistent representation of the HTML report being created is stored and accessible in the .reportDOM field of HTMLReportRef objects
[[ and [[<- methods created for HTMLReportRef objects which allow selection, replacement and insertion of objects directly into reports
Publish generic now accepts a ‘name’ argument.
Existing reports can be read in via readReport, modified (via publish, [[<-, or direct manipulation of .reportDOM), and rewritten to file
Path generic now returns a list/vector of the location slot values of the attached ReportHandlers object(s). These can be paths, connections, or other indications of report destination.
Link generic function provided to build tables/sets of HTML links
Added support for publishing ggbio and recordedplot objects
CSS changed to Twitter Bootstrap
Bugfixes to how NAs are handled when filtering and sorting columns
New methods to handle output from running a glmLRT test in edgeR or nbinomTest in DESeq
DEPRECATED: HTMLReport class is superseded by HTMLReportRef
DEPRECATED: publication of HTMLReportRefs directly to a report (in order to make an index page) is no longer supported. Use the Link function.
DEPRECATED: the page generic is not meaningful for HTMLReportRef objects (not all of which have a corresponding connection) and is deprecated. Use path instead.

Rgraphviz

Changes in version 2.5:

Expose mai argument in plot,Ragraph-method.
Changed the LICENSE to EPL.
Fixed some wrong text in the DESCRIPTION file.
Fixed pieGylph to adress the issue of warning messages about rep(NULL) (reported by Cristobal Fresno Rodríguez Cristobalfresno@gmail.com).
Updated Imports, Depends, NAMESPACE as per R CMD check requirements.
Fixing issue with the lt~obsolete.m4 file(s) in Graphviz; R CMD check was issueing a warning.
Moved vignettes from inst/doc to vignettes directory.

rhdf5

Changes in version 2.6.0:

NEW FEATURES

support for logical added
support for reading attributes added (use read.attributes=TRUE)
enabeled compression for data.frame in h5write

USER VISIBLE CHANGES

Use BiocStyles for package vignette

Risa

1.3.3: 1. Fixed definitions of assay.filenames.per.sample and factors. 2. Fixed regulession of investigation file (i_) to be considered at the beginning of the string. 3. Added CITATION file.

RNASeqPower

Changes in version 1.0.1:

Add a citation to the manual page, add CITATION file

rols

Changes in version 1.3.2:

fixed bug in isIdObsolete, reported by Alex Thomas <2013-07-27 Sat>

Changes in version 1.3.1:

other example in CVParam-class example, as PSI ontology is not available <2013-05-02 Thu>

Changes in version 1.3.0:

Bioc 2.13 devel version bump

ROntoTools

Changes in version 1.2.0:

add the ability to analyze gene sets (pathways with no interaction) using only over-representation
bug fixes: plot boundaries, etc.

rqubic

Changes in version 1.8.1 (2011-08-02):

Fix errors in documentations

Changes in version 1.8.0 (2011-07-11):

Submission to Bioconductor

Rsamtools

Changes in version 1.14.0:

NEW FEATURES

seqinfo(FaFile) returns available information on sequences and lengths on Fa (indexed fasta) files.
filterBam accepts FilterRules call-backs for arbitrary filtering.
add isIncomplete,BamFile-method to test for end-of-file
add count.mapped.reads to summarizeOverlaps,*,BamFileList-method; set to TRUE to collect read and nucleotide counts via countBam.
add summarizeOverlaps,*,character-method to count simple file paths
add sequenceLayer() and stackStringsFromBam()
add ‘with.which_label’ arg to readGAlignmentsFromBam(), readGappedReadsFromBam(), readGAlignmentPairsFromBam(), and readGAlignmentsListFromBam()

SIGNIFICANT USER-VISIBLE CHANGES

rename: readBamGappedAlignments() -> readGAlignmentsFromBam() readBamGappedReads() -> readGappedReadsFromBam() readBamGappedAlignmentPairs() -> readGAlignmentPairsFromBam() readBamGAlignmentsList() -> readGAlignmentsListFromBam() makeGappedAlignmentPairs() -> makeGAlignmentPairs()
speedup findMateAlignment()

DEPRECATED AND DEFUNCT

deprecate readBamGappedAlignments(), readBamGappedReads(), readBamGappedAlignmentPairs(), readBamGAlignmentsList(), and makeGappedAlignmentPairs()

BUG FIXES

scanVcfHeader tolerates records without ID fields, and with fields named similar to ID.
close razip files only once.
report tabix input errors

rSFFreader

Rsubread

Changes in version 1.12.0:

NEW FEATURES

Added a number of new features to featureCounts read summarization function, including reordering of reads in BAM files to make reads from the same pair be adjacent to each other, support for chromosome aliases and output of complete annotation data for counting results from meta-feature level summarization.

NEW FEATURES

It is described in more details in the Users Guide on how featureCounts program summarizes reads.

NEW FEATURES

Improved short indel detection for both Subread (align function) and Subjunc aligners. This was achieved by building a consensus indel table and by realigning the reads. Discovered indels are reported in the output in addition to the read mapping results.

NEW FEATURES

Support for detection of long indels (up to 200bp) was added in Subread. When the specified value of `indels’ argument is greater than 16, Subread will automatically perform read assembly to detect long insertions and deletions.

NEW FEATURES

Subread and Subjunc can now take FASTQ/FASTA, SAM and BAM files as input and output mapping results in both SAM and BAM formats.

NEW FEATURES

Subjunc now directly operates on raw read data (it previously took Subread output as input), thus reducing running time by nearly half.

NEW FEATURES

Subjunc can be instructed to output uniquely mapped reads. Hamming distance and mapping quality scores can be used to break ties when more than one best location was found.

NEW FEATURES

More options were added to exactSNP program. Its documentation was also greatly improved.

NEW FEATURES

A number of bug fixes.

rTANDEM

Changes in version 1.1.6:

NEW FEATURES

rTANDEM is now based on x!tandem version 13-09-01 ‘sledgehammer’

Changes in version 1.1.5:

BUG FIXES

Fixed a memory management problen in Cpp

NEW FEATURES

More parameters are supported.

Changes in version 1.1.4:

NEW FEATURES

rTANDEM is now based on x!tandem version 13-06-15 ‘jackhammer’

BUG FIXES

Corrected a bug that prevented the use of multi-threading
Corrected a bug that could affect results when multiple fasta files are assigned to a same taxon.

RTCA

Changes in version 2009-07-13:

combineRTCA(list): Additional column is renamed into Plate. The vlues is evaluated from list item names. When the list has no name, an integer index beginning from 1 is used. Special attentions to list partially with names is noted in the documentation.
parseRTCA(file, dec=”.”,phenoData, skipWell,…): Example is added in the documentation how to import pre-configured phenoData. Details section in the documentation is re-written to describe the process of parsing.
RTCA-class: Experiment ID added to RTCA class
Makefile: add Makefile to simplify common tasks like check and install
plotGridEffect: takes ‘column’ instead of ‘col’ as mode parameter, and renders the mode as the title of the legend. Documentation updated.
plotRTCA: is removed from the package and is substituted by the plot function.

RTN

Changes in version 1.0.0:

1st Bioconductor release of RTN [2013-10-15].

rtracklayer

Changes in version 1.22:

NEW FEATURES

import,BigWigFile gains an asRle parameter that returns the data as an RleList (assuming it tiles the sequence); much faster than importing a GRanges and calling coverage() on it.
add export,RleList,BigWigFile method for direct (and much more efficient) output of RleLists (like coverage) to BigWig files.

SIGNIFICANT USER-VISIBLE CHANGES

UCSCData now extends GRanges instead of RangedData (thanks Herve)

BUG FIXES

handle different Set-Cookie header field casing; often due to proxies (thanks to Altuna Akalin)
attempt to more gracefully handle UCSC truncation of large data downloads
handle re-directs due to UCSC mirroring (thanks Martin Morgan)

rTRM

Changes in version 1.0:

First release in Bioconductor.
Integration with Bioconductor packages: MotifDb and PWMEnrich, graph (limited).
Human and mouse BioGRID datasets updated to version 3.2.105 (October 2013).

rTRMui

Changes in version 1.0:

First Bioconductor release.
Provides a shiny interface to rTRM.
All options available in rTRM can be accesses from rTRMui.
Several utilities to control network appearance (node, edge and label size, etc.)
Download results in PDF and text format.

SBMLR

Changes in version 1.57.1:

NEW FEATURES

Added new function S4toS3() for converting S4 SBML models of rsbml into S3 SBMLR models.
Includes code from Vishak Venkateswaran’s branch of SBMLR on github (July 2011). This is may allow it to read more models in http://www.ebi.ac.uk/biomodels-main/ I say may because I don’t fully understand all of his codes, but add it in anyway.
Problem of libsbml allowing multiple args to multiplication operator was solved by using prod(). Similarly for sum(). Note that “*”() is strictly a binary operator.

SIGNIFICANT USER-LEVEL CHANGES

Call my model object call SBMLR now to let SBML refer to rsbml’s SBML object. Similary my simulate() is now sim() to keep it clear of rsbml’s simulate().
SBMLR model files no longer need to have the reversible flag set. The default is FALSE, which is the opposite of Level 2: all of my reaction rate laws have always been positive, and a design objective I like is to keep SBMLR model files as lean as possible (subject to the constraint that they be valid R code).
Simulate handles lsoda() event dataframes, see simulate help.
curtoNatural.R (see Fig. 7 BMC Bioinformatics 2004, 5:190) is now in the models folder.
The SOD model of Kowald et al, JTB 238 (2006) 828–840 is now also in this folder.
Two pdfs of publications that are freely available were removed to make the package lighter.
Similarly, only manual.doc remains: its redundant pdf is now out.

Notes

SBMLR objects do need to have their reversible flag set in files, but do in SBMLR objects in R.

SCAN.UPC

Changes in version 2.2.8:

NEW FEATURES

Ability to download microarray data directly from Gene Expression Omnibus and normalize the files in a single command.
Alternate functions (SCANfast and UPCfast) for performing SCAN and UPC normalization that use fewer probes and thus execute in ~60% less time.
Ability to execute normalize multiple .CEL files in parallel either across multiple cores on a single computer or across multiple computers on a cluster.
Ability to generate RNA-Seq annotation files to be used with the UPC_RNASeq function from GTF/FASTA source files.
Ability to download and install BrainArray packages via an R function.
Improved support for Affymetrix exon arrays.
Improved support for Affymetrix HT_HG-U133A early access exon arrays.

OTHER

Various improvements and clarifications to the docs.

SeqArray

Changes in version 1.1.5:

minor bug fix in asVCF
update man page “SeqVarGDSClass-class.Rd” with new methods
in DESCRIPTION, BiocGenerics listed in “Suggests” instead of “Imports” as suggested by R CMD check
bug fix in seqDelete
revise the function ‘seqTranspose’ according to the update of gdsfmt (v1.0.0)

Changes in version 1.1.4:

add a new argument “action” to the function ‘seqSetFilter’
add a new function ‘seqInfoNewVar’ which allows adding new variables to the INFO fields

Changes in version 1.1.3:

minor bug fix to avoid ‘seqGetData’ crashing when no value returned from a variable-length variable
update documents

Changes in version 1.1.2:

added methods ‘qual’, ‘filt’, ‘asVCF’
‘granges’ method uses length of reference allele to set width

Changes in version 1.1.1:

revise the argument ‘var.index’ in the function ‘seqApply’
basic supports of ‘GRanges’ and ‘DNAStringSetList’

SeqGSEA

Changes in version 1.1.5 (2013-09-01):

Added an all-in function runSeqGSEA() for one step analysis
Modified genpermuteMat() with invoking set.seed() for reproducibility
Vignette updated

Changes in version 1.1.4 (2013-08-10):

Updated functions to allow DE-only GSEA analysis.
Fixed a few bugs.
Vignette updated.

Changes in version 1.1.3 (2013-06-13):

Sorted out an error due to biomaRt update (thanks to Martin Morgan).

Changes in version 1.1.2 (2013-05-01):

Updated vignette.

Changes in version 1.1.1 (2013-04-23):

The methodology paper of the SeqGSEA package published at BMC Bioinformatics (2013, 14(Suppl 5):S16).
Added a function writeScores to generate DE/DS and gene scores output.

shinyTANDEM

Changes in version 0.99.1:

NEW FEATURES

It is now possible to use a rTResult object from the R session as a parameter to the shinyTANDEM function.

Changes in version 0.99.0:

First submission of shinyTANDEM to Bioconductor

ShortRead

Changes in version 1.19:

SIGNIFICANT USER-VISIBLE CHANGES

qa(…, type=”fastq”) uses a sample of n=1000000 reads by default, rather than then entire file; use sample=FALSE to revert to previous behavior.

NEW FEATURES

encoding,FastqQuality and encoding,SFastqQuality provide a convenient map between letter encodings and their corresponding integer quality values.
filterFastq transforms one fastq file to another, removing reads or nucleotides via a user-specified function. trimEnds,character-method & friends use this for an easy way to remove low-quality base.

BUG FIXES

writeFastq successfully writes zero-length fastq files.
FastqStreamer / FastqSampler warn on incomplete (corrupt) files

SpacePAC

Changes in version 0.99.0:

First release of the SpacePAC package.
Two 3D clustering methods: Using a Simulation approach and using a Poisson approach.
Allows a rudimentary plotting function to visualize the most significant cluster. Currently only one sphere can be plotted at a time.

spliceR

Changes in version 1.0.0:

Initial release.

supraHex

Changes in version 1.0.0:

NEW FEATURES

A pure R implementation of a self-organising learning algorithm as applied to the symmetric topology of the supra-hexagonal map

NEW FEATURES

Dozens of functions for post-processing the trained map with multiple purposes, including: (i) visualizations of map indexes, hits and patterns; (ii) partitioning of the map into continuous clusters (i.e. gene meta-clusters) as they are different from gene clusters in an individual map node; and (iii) reordering of sample-specific map components (i.e. sample correlation)

NEW FEATURES

Several omics datasets used to illustrate the functionalities supported in supraHex

synapter

Changes in version 1.3.4:

estimateMasterFdr now support list of vector as pepfiles <2013-09-27 Fri>
import(MSnbase) <2013-09-27 Fri>

Changes in version 1.3.3:

Updated references. <2013-07-05 Fri>

Changes in version 1.3.2:

fixed bug when using findEMRTs = “copy” <2013-05-30 Thu>

Changes in version 1.3.1:

Reporting total number of peptides in dbUniquePeptideSet. Fixes issue #41. <2013-05-13 Mon>
New mergedEMRTs arg in findEMRTs. Closes issue #38. <2013-05-13 Mon>
fixed synapterTiny$QuantPep3DData, which had the rownames as first column synapterTiny$QuantPep3DData$X. Detected thanks to new mergedEMRTs arg. <2013-05-13 Mon>
added mergedEMRTs arg to synergise <2013-05-22 Wed>
Synapter checks that one file per list element is passed <2013-05-28 Tue>
minor typo/fixes <2013-05-28 Tue>
new idSource column when matching EMRTs <2013-05-29 Wed>
new performance2 method that shows identification source and NA values contingency table <2013-05-29 Wed>
new filterPeptideLength method <2013-05-29 Wed>
added peplen argument to synergise to filter on peptide length <2013-05-29 Wed>

Changes in version 1.3.0:

Bioc 2.13 devel version bump

TargetSearch

Changes in version 1.18.0:

NEW FEATURES

New options for function ‘ProfileCleanUp’ that allow fine tuning of the suggested metabolite in case of redundancy. This problem occurs when the reference library contains two or more metabolites in the same retention time window.

NEW FEATURES

The function ‘Write.Results’ can create a quantification matrix based in one quantification mass. This mass can be selected automatically or specified by the user.

NEW FEATURES

The above options have been incorporated in the GUI as well.

TCC

Changes in version 1.2.0:

NEW FEATURES

This package was released as a Bioconductor package (previously CRAN).
WAD method for identifying DEGs was added.
ROKU method for identifying tissue-specific genes was added.
‘increment’ argument of ‘calcNormFactor’ function was added.

SIGNIFICANT USER-VISIBLE CHANGES

‘replicates’ field of TCC class was deleted.

Changes in version 1.1.3:

SIGNIFICANT USER-VISIBLE CHANGES

‘generateSimulationData’ function was renamed to ‘simulateReadCount’.

SIGNIFICANT USER-VISIBLE CHANGES

‘names’ field of TCC class was changed to ‘gene_id’.

SIGNIFICANT USER-VISIBLE CHANGES

‘hypoData’ was reduced to a smaller data set.

SIGNIFICANT USER-VISIBLE CHANGES

‘hypoData_mg’ was created. This is the simulation dataset which consists of 1,000 genes and 9 samples.

Changes in version 1.0.0:

SIGNIFICANT USER-VISIBLE CHANGES

‘TCC’ class was implemented as a R5 reference class. Wrapper functions with functional programming semantics were proviede.

TEQC

Changes in version 3.0.0:

new function ‘multiTEQCreport’ collects results from ‘TEQCreport’ output from multiple samples and creates a combined quality report

Changes in version 2.9.2:

bug fix in ‘coverage.target’: when getting reads data from a BAM file, output of average coverage values per target was wrong (in wrong order)

tigre

Changes in version 1.14.1:

BUG FIXES

Various fixes for non-cascade ODE model (i.e. model not using TF mRNA data) (thanks to Andrea Ocone for the report)

TransView

Changes in version 1.5.9:

BUG FIXES

Use of mcols in favor of values to access meta data in GRanges objects

Changes in version 1.5.8:

BUG FIXES

Minor bug fix in annotatePeaks to accommodate recent changes in GRanges

Changes in version 1.5.7:

BUG FIXES

Minor bug fix in annotatePeaks

Changes in version 1.5.6:

BUG FIXES

Minor bug fix

Changes in version 1.5.5:

BUG FIXES

Speed improvement and improved accuracy of annotatePeaks

Changes in version 1.5.4:

NEW FEATURES

plotTV can now plot expression profiles including introns triggered by the new option pre_mRNA

BUG FIXES

Fixed a bug which occurred if only two colors were passed to plotTV via colr

Changes in version 1.5.3:

NEW FEATURES

meltPeak can return loess smoothed scores.

Changes in version 1.5.2:

BUG FIXES

Fixed an issue with the gene names returned from gtf2gr.

Changes in version 1.5.1:

BUG FIXES

The q-value cut off in macs2gr did not work as expected.

triplex

Changes in version 1.2.0:

NEW FEATURES

It’s now possible to set custom scoring and isogroup tables through triplex.search interface.

NEW FEATURES

New triplex.score.table and triplex.group.table functions for getting default scoring and isogroup tables to make the customization process almost effortless. OPTIMIZATIONS

NEW FEATURES

Dynamic algorithm optimization technique implemented as a computational reduction based on minimal score option.

NEW FEATURES

Optimized usage of processor data cache - the computation was divided into smaller pieces to prevent cache misses.

VariantAnnotation

Changes in version 1.8.0:

NEW FEATURES

Add ‘upstream’ and ‘downstream’ arguments to IntergenicVariants() constructor.
Add ‘samples’ argument to ScanVcfParam().
Add readGT(), readGeno() and readInfo().
Add VRanges, VRangesList, SimpleVRangesList, and CompressedVRangesList classes.
Add coercion VRanges -> VCF and VCF -> VRanges.
Add methods for VRanges family: altDepth(), refDepth(), totalDepth(), altFraction() called(), hardFilters(), sampleNames(), softFilterMatrix() isIndel(), resetFilter().
Add stackedSamples,VRangesList method.

MODIFICATIONS

VCF validity method now requires the number of rows in info() to match the length of rowData().
PRECEDEID and FOLLOWID from locateVariants() are now CharacterLists with all genes in ‘upstream’ and ‘downstream’ range.
Modify rownames on rowData() GRanges to CHRAM:POS_REF/ALT for variants with no ID.
readVcf() returns info() and geno() in the order specified in the ScanVcfParam.
Work on scanVcf(): - free parse memory at first opportunity - define it_next in .c rather than .h - parse ALT “.” in C - hash incoming strings - parse only param-requested ‘fixed’, ‘info’, ‘geno’ fields
Add dimnames<-,VCF method to prevent ‘fixed’ fields from being copied into ‘rowData’ when new rownames or colnames were assigned.
Support read/write for an emtpy VCF.
readVcf(file=character, …) method attempts coercion to TabixFile.
Support for read/write an emtpy VCF.
Add performance section to vignette; convert to BiocStyle.
expand,CompressedVcf method expands geno() field ‘AD’ to length ALT +
1. The expanded field is a (n x y x 2) array.
‘genome’ argument to readVcf() can be a character(1) or Seqinfo object.

DEPRECATED and DEFUNCT

Defunct dbSNPFilter(), regionFilter() and MatrixToSnpMatrix().
Deprecate readVcfLongForm().

BUG FIXES

Fix bug in compatibility of read/writeVcf() when no INFO are columns present.
Fix bug in locateVariants() when ‘features’ has no txid and cdsid.
Fix bug in asVCF() when writing header lines.
Fix bug in “expand” methods for VCF to handle multiple ‘A’ columns in info().

VariantTools

Changes in version 1.4:

NEW FEATURES

tallyVariants will now keep ref rows if variant_strand=0; this is useful for getting information when no alts are present (e.g., for making wildtype calls). Better have a big cluster to do this over the whole genome.
add a keep_extra_stats param to TallyVariantsParam; setting this to FALSE will speed things up when the extra stats are not needed.
idVerify now supports VCF input like that output by GATK.
callableFraction() now supports GRangesList and TranscriptDb.

USER-VISIBLE CHANGES

The API is now based on VRanges, a formal GRanges-derived class for representing variants; use of so-called “tally” or “variant” GRanges is deprecated.
Disable proximity filter by default; we recommend this now only for whole genome calling.
QA filtering is no longer a formal part of the calling pipeline; we recommend to apply QA filters “softly” via qaVariants() and use the results for diagnostics only.
Use BiocParallel (BPPARAM argument) for tallyVariants
VariantTallyParam deprecated; use TallyVariantsParam

BUG FIXES

idVerify now correctly computes cliques instead of connected components
use the total count, rather than the ref count when calculating the alt frequency

xcms

Changes in version 1.37.6:

NEW FEATURE

Introducing write.mzQuantML(xcmsSet) to export the peak list and grouped matrix to the PSI format mzQuantML (see http://www.psidev.info/mzquantml)

USER VISIBLE CHANGES

Add Brigham Young University to LICENSE file for copyright purposes.
Add copyright information display when running findPeaks.massifquant() within xcmsRaw.R
Clean and update documentation for findPeaks.massifquant-methods.Rd

BUG FIXES

Remove unused parameters in findKalmanROIs() within xcmsRaw.R

Changes in version 1.37.5:

BUG FIXES

fixed bug in retcor.obiwarp where the scanrange of the first sample would be checked instead of the center sample

Changes in version 1.37.4:

BUG FIXES

Skip t-test in diffreport() if one class has less than 2 samples.

Changes in version 1.37.3:

BUG FIXES

fixed bug in patternVsRowScore (group.nearest) that was introduced by the modifications in rev 65169 and caused features to be aligned that were far outside the given m/z and retention time windows.

Changes in version 1.37.1:

BUG FIXES

fixed fillPeaks, which 1) dropped non-standard columns and 2) failed if nothing to do, based on patches by Tony Larson.

NEW FEATURES

Introducing msn2xcmsRaw, to allow findPeaks() on MS2 and MSn data

xps

Changes in version 3.00:

VERSION xps-1.21.5

add QualTreeSet methods NUSE() and RLE() to get stats and values
update man export.Rd

VERSION xps-1.21.4

update xpsQAReport.R for R-3.x

VERSION xps-1.21.3

update XPSSchemes.cxx to replace error with warning for missing annotation header ‘%netaffx-annotation-‘

VERSION xps-1.21.2

update XPSNormalizer.cxx to correct for uninitialized variables

VERSION xps-1.21.1

update README
update Makefile to set include path (for ~/.R/Makevars)
update XPSUtils.cxx to eliminate warning with clang

VERSION xps-1.19.10

update XPSSchemes.cxx to correct possible memory error in TString array names[i]

VERSION xps-1.19.9

update README

VERSION xps-1.19.8

replace .path.package() with path.package()

VERSION xps-1.19.7

update XPSSchemes.cxx to replace error with warning for missing annotation header ‘%genome-species’

VERSION xps-1.19.2 - 6

update configure.win and Makefile.win for ROOT compiled with MinGW; xps works now on Windows 7

VERSION xps-1.19.1

update Import..Annotation() methods in XPSchemes.cxx to protect against tabs in Affymetrix annotation files
update script4schemes.R to include schemes with annotation na33

Changes in version 2.15:

VERSION xps-1.17.2

update script4schemes.R to include schemes for HuGene-2_x-st arrays
update script4xps.R with example 4a for HuGene-2_1-st arrays
update README

VERSION xps-1.17.1

remove warnings: partial argument match
zzz.R: use .onAttach()

VERSION xps-1.15.2

move to ROOT version 5.32/01, update README

VERSION xps-1.15.1

update zzz.R

Changes in version 2.14.0:

VERSION xps-1.13.10

update function xpsQAReport() to replace “_” with “_” for *.Rnw

VERSION xps-1.13.9

add quality report function xpsQAReport()
update vignette xps.Rnw

VERSION xps-1.13.8

add functions attachProbe(), removeProbe(), etc.
add functions contentGC(), probeSequence()
add functions inten2GCplot(), plotInten2GC()
update vignette xps.Rnw

VERSION xps-1.13.7

add function unitID2symbol()
add function plotProbeset()
update vignette xps.Rnw

VERSION xps-1.13.6

update function indexUnits() for exon probesets
add function symbol2unitID()
add function probesetplot()

VERSION xps-1.13.5

update script4schemes.R to include schemes with annotation na32
update script4xps.R and script4exon.R

VERSION xps-1.13.4

move to ROOT version 5.30/00, update README
update vignettes xps.Rnw and xpsClasses.Rnw

VERSION xps-1.13.3

correct problem in unitID2affyID() on Linux caused by sQuote()

VERSION xps-1.13.2

add functions plotXXX()
function hist() no longer requires to attachInten()
add functions indexUnits(), pmindex(), mmindex()
add functions probesetID2unitID(), unitID2probesetID(), etc
add functions attachUnitNames(), removeUnitNames()
add functions attachDataXY(), removeDataXY()

VERSION xps-1.13.1

update function plotImage() to draw background images

Changes in version 2.13.0:

VERSION xps-1.11.12

update functions: plotBoxplot(), plotAffyRNAdeg()

VERSION xps-1.11.11

update functions: plotImage(), plotAffyRNAdeg()

VERSION xps-1.11.10

add functions: plotImage(), plotBoxplot()
update methods image()

VERSION xps-1.11.9

add method: pcaplot()
update method plotAffyRNAdeg()

VERSION xps-1.11.8

add methods: corplot(), madplot()

VERSION xps-1.11.7

update method plotAffyRNAdeg()

VERSION xps-1.11.6

add methods for RNA degradation plots: xpsRNAdeg(), plotAffyRNAdeg()
add man pages

VERSION xps-1.11.5

correct minor bug in XPSProcessing.cxx: ExportExprTreeInfo()
update method image()
add man pages

VERSION xps-1.11.4

add new class QualTreeSet to add quality control features
add functions qualify() and fitQC() and derived functions
add method image() for residual plots of IVT, Gene ST, Exon ST and plate arrays
add new plots coiplot() and borderplot()
update boxplot(), callplot(), image() to be independent of slot ‘data’

VERSION xps-1.11.3

add function trma()

VERSION xps-1.11.1

update DESCRIPTION to correct SystemRequirements to root_v5.27.04
update function READ_WSTRING() to handle big endian for PPC

Changes in version 2.12.0:

VERSION xps-1.9.9

update method XExonChip::ProbesetLevel() for whole genome annotation na31 files

VERSION xps-1.9.8

revert update of Makefile.win

VERSION xps-1.9.7

update Makefile.win to clean xpsLinkDef.h
update script4schemes.R for annotation na31 (updated release)

VERSION xps-1.9.6

update information files for new ROOT Version 5.27/04 (root_v5.27/04)
update script4xps.R, script4schemes.R for annotation na31

VERSION xps-1.9.5

update import.data to use make.names(celnames) to protect against certain characters

VERSION xps-1.9.4

update root.profile.R, macroDrawProfilePlot.C to allow selecting subset of trees
in read.table() set stringsAsFactors=FALSE

VERSION xps-1.9.3

update method XPreFilter::Calculate() to handle exon arrays correctly

VERSION xps-1.9.2

update Makefile and Makefile.arch

VERSION xps-1.9.1

add support in XPSAnalysis.cxx to export exon array probeset annotations (filters)

Changes in version 2.11.0:

VERSION xps-1.7.9

update method validData() to handle slot data containing different column types
update methods seExprTreeSet(), rleplot(), mvaplot(), nuseplot()

VERSION xps-1.7.8

add method xpsFIRMA()
add functions firma(), firma.expr(), firma.score()

VERSION xps-1.7.7

update bgcorrect.R to warn from using tmpdir resulting in empty root file
update normalize.R to warn from using tmpdir resulting in empty root file

VERSION xps-1.7.6

minor change to allow computation with g++ 4.4.x

VERSION xps-1.7.4

add NEWS

VERSION xps-1.7.3

add ExprTreeSet methods validSE(), nuseplot(), rleplot()
allow to export layout trees for incomplete *.CLF files
update examples/updateAnnotation.R

VERSION xps-1.7.2

add examples/updateAnnotation.R
update script4xps.R

VERSION xps-1.7.1

allow using mas5() and mas5.call() with plate arrays w/o MMs
update script4xps.R

Changes in version 2.10.0:

VERSION xps-1.5.19

update script4xps.R

VERSION xps-1.5.18

add parameter bgcorrect.option to function mas5.call()

VERSION xps-1.5.17

update README

VERSION xps-1.5.16

allow handling of probesets w/o MMs on Citrus.CDF

VERSION xps-1.5.15

validBgrd() implement ‘which’
add vignette xpsPreprocess.pdf
add example/macro4xpsPreprocess.R

VERSION xps-1.5.14

update export() to include read.table(..,comment.char=’’)
update methods.DataTreeSet.R to allow probe-level lowess and supsmu normalization

VERSION xps-1.5.13

update express() to allow setting bufsize for tree baskets

VERSION xps-1.5.12

changes to allow import of miRNA-1_0.CDF

VERSION xps-1.5.9

update validOption() to allow ‘separate:none’

VERSION xps-1.5.8

update rma() to allow improved ties handling as option like preprocessCore

VERSION xps-1.5.7

update method validCall()
add methods validExpr() and validPVal()
update vignette APTvsXPS.pdf
update examples script4xps2apt.R and script4bestmatch.R

VERSION xps-1.5.4

update function exonLevel() to use affx=c(4,8,16,32)
update function dataDataTreeSet() to return correct ids for mask
add new internal function exonLevelIDs()

VERSION xps-1.5.3

update help file exonLevel.Rd

VERSION xps-1.5.1

update validData() to check for duplicate rownames
allow reading of genetitan plate data

Changes in version 2.9.0:

VERSION xps-1.3.13

update DESCRIPTION to mention root version
update README

VERSION xps-1.3.12

correct bug in implementation of FDR and Hochberg

VERSION xps-1.3.11

make function exonLevel public and add exonLevel.Rd

VERSION xps-1.3.8

update all initialize methods to prevent checkS3forClass warnings
update bgcorrect.rma, bgcorrect.mas5
update script4xps.R, script4exon.R

VERSION xps-1.3.6

support using genome array as exon arrays

VERSION xps-1.3.5

add code in function import.data() to replace dots, colons in celnames with underscores

VERSION xps-1.3.4

correct bug in xpsPreprocess for add.data=FALSE
correct sub(.root, .txt, x) to sub(.root, .txt, x)
update root.image() to get setname from setName()

VERSION xps-1.3.3

change intensity<- to allow using slot data for further processing

VERSION xps-1.3.1

add function root.merge.data()

Changes in version 2.8.0:

VERSION xps-1.1.9

protect class XRMABackground against defect Affy chips, e.g. zero division
protect root.data() etc against duplicate celnames or treenames

VERSION xps-1.1.8

correct bug in class XINICall resulting in buffer overflow

VERSION xps-1.1.7

add call method I/NI-call (Talloen et al)

VERSION xps-1.1.6

prevent import of CEL-files with zero max intensity
update functions returning ExprTreeSet to import results as option only
update functions returning CallTreeSet to import results as option only
update root.density etc to allow saving from R function
add root.profile to use root graphics for boxplots
add summarization method FARMS (Hochreiter et al)
add summarization method DFW (Chen et al)
update vignette xps.pdf

VERSION xps-1.1.5

correct problem in validData for CEL-files starting with numbers

VERSION xps-1.1.4

update vignette xps.pdf
add new vignette APTvsXPS.pdf
update examples script4exon.R
add examples script4xps2apt.R and script4bestmatch.R
update README

VERSION xps-1.1.3

to allow CEL-names starting with a number, update to read.table(…, check.names=FALSE)
update ExprTreeSet to set slot exprtype to correct type
add functions root.expr() and root.call()
need to change setname for dabg.call() from CallTreeSet to CallSet as for mas5.call()

VERSION xps-1.1.2

allow different exonlevels for bgrd, normalization, summarization
update replacement methods exprs, pvalData, presCall to allow subsetting
add function metaProbesets to compute metacoreList.mps for apt

VERSION xps-1.1.1

increase maximum root file size from 2GB to 2TB
decrease computation time
correct bug preventing export of exon probeset normalized data

Changes in version 2.7.0:

VERSION xps-0.99.11

correct bug resulting in empty exon probeset column

VERSION xps-0.99.10

update source code to handle tmpdir correctly on WinXP
update examples script4xps.R and script4exon.R

VERSION xps-0.99.9

update methods namePart, extenPart, validData, validBgrd to handle names with underscores

VERSION xps-0.99.8

update functions root.xxx to work with WinXP

VERSION xps-0.99.3

package can now be built for Windows XP
added possibility to add current date and/or time to root filename
added function existsROOTFile
updated vignette xps.Snw

VERSION xps-0.4.3

new method rawCELName() to get the names of the imported CEL-files

VERSION xps-0.4.2

add support to import generic (calvin) CEL-files
update method volcanoplot

VERSION xps-0.4.1

change DESCRIPTION
add method volcanoplot
correct update bug in xpsUniFilter

VERSION xps-0.4.0

import.data: import CEL-files from different directories
update DESCRIPTION, NAMESPACE
add possibility to apply non-sepcific filters and univariate filters
add S4 classes Filter, PreFilter, UniFilter
add S4 classes FilterTreeSet and AnalysisTreeSet

Packages removed from the release

The following packages are no longer in the release:

dualKS, externalVector, GeneGroupAnalysis, iFlow, KEGGSOAP, xmapcore

Contents

Getting Started with Bioconductor 2.13

New Software Packages

NEWS from new and existing packages

ADaCGH2

affxparser

annmap

AnnotationHub

aroma.light

ASSET

BAGS

BaseSpaceR

BiGGR

bigmemoryExtras

bioassayR

Biobase

BiocParallel

BiocStyle

biomvRCNS

BitSeq

bsseq

bumphunter

CAMERA

categoryCompare

CellNOptR

ChemmineOB

chimera

chipenrich

ChIPpeakAnno

cisPath

cleaver

clonotypeR

clusterProfiler

CNAnorm

CNORfuzzy

codelink

DART

deepSNV

deltaGseg

DESeq2

DEXSeq

DiffBind

DOSE

DSS

EBImage

edgeR

eiR

fabia

FGNet

flowType

fmcsR

gage

gCMAP

gCMAPWeb

geNetClassifier

GeneticsPed

GenomicFeatures

GenomicRanges

GGtools

gmapR

GOSemSim

GSEABase

GWASTools

hapFabia

HiTC

hpar

HTSeqGenie

htSeqTools

HTSFilter

hyperdraw

illuminaio

imageHTS

intansv

iPAC

IPPD

IRanges

isobar

KEGGgraph

KEGGprofile

lmdme