| Package | Maintainer | Title |
|---|---|---|
| ABarray | Yongming Andrew Sun | Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Micorarray (AB1700) gene expression data. |
| ADaCGH2 | Ramon Diaz-Uriarte | Analysis of data from aCGH experiments using parallel computing and ff objects |
| adSplit | Claudio Lottaz | Annotation-Driven Clustering |
| affy | Rafael A. Irizarry | Methods for Affymetrix Oligonucleotide Arrays |
| affycomp | Rafael A. Irizarry | Graphics Toolbox for Assessment of Affymetrix Expression Measures |
| AffyCompatible | Martin Morgan | Affymetrix GeneChip software compatibility |
| affycoretools | James W. MacDonald | Functions useful for those doing repetitive analyses with Affymetrix GeneChips. |
| AffyExpress | Xuejun Arthur Li | Affymetrix Quality Assessment and Analysis Tool |
| affyILM | Myriam Kroll and Fabrice Berger | Linear Model of background subtraction and the Langmuir isotherm |
| affyio | Benjamin Milo Bolstad | Tools for parsing Affymetrix data files |
| affylmGUI | Keith Satterley | GUI for affy analysis using limma package |
| affyPara | Markus Schmidberger | Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays |
| affypdnn | Laurent Gautier | Probe Dependent Nearest Neighbours (PDNN) for the affy package |
| affyPLM | Ben Bolstad | Methods for fitting probe-level models |
| affyQCReport | Craig Parman | QC Report Generation for affyBatch objects |
| AffyTiling | Charles G. Danko | Easy extraction of individual probes in Affymetrix tiling arrays |
| Agi4x44PreProcess | Pedro Lopez-Romero | PreProcessing of Agilent 4x44 array data |
| AgiMicroRna | Pedro Lopez-Romero | Processing and Differential Expression Analysis of Agilent microRNA chips |
| altcdfenvs | Laurent Gautier | alternative CDF environments (aka probeset mappings) |
| annaffy | Colin A. Smith | Annotation tools for Affymetrix biological metadata |
| annotationTools | Alexandre Kuhn | Annotate microarrays and perform cross-species gene expression analyses using flat file databases. |
| apComplex | Denise Scholtens | Estimate protein complex membership using AP-MS protein data |
| aroma.light | Henrik Bengtsson | Light-weight methods for normalization and visualization of microarray data using only basic R data types |
| ArrayExpress | Audrey Kauffmann | Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet |
| arrayMvout | V. Carey | multivariate outlier detection for expression array QA |
| arrayQuality | Agnes Paquet | Assessing array quality on spotted arrays |
| arrayQualityMetrics | Audrey Kauffmann | Quality metrics on microarray data sets |
| ArrayTools | Arthur Li | geneChip Analysis Package |
| BAC | Raphael Gottardo | Bayesian Analysis of Chip-chip experiment |
| BayesPeak | Jonathan Cairns | Bayesian Analysis of ChIP-seq Data |
| baySeq | Thomas J. Hardcastle | Empirical Bayesian analysis of patterns of differential expression in count data |
| beadarray | Mark Dunning | Quality assessment and low-level analysis for Illumina BeadArray data |
| beadarraySNP | Jan Oosting | Normalization and reporting of Illumina SNP bead arrays |
| BeadDataPackR | Mike Smith | Compression of Illumina BeadArray data |
| betr | Martin Aryee | Identify differentially expressed genes in microarray time-course data |
| BGmix | Alex Lewin | Bayesian models for differential gene expression |
| bgx | Ernest Turro | Bayesian Gene eXpression |
| BHC | Rich Savage | Bayesian Hierarchical Clustering |
| BicARE | Pierre Gestraud | Biclustering Analysis and Results Exploration |
| BioNet | Marcus Dittrich | Routines for the functional analysis of biological networks |
| bridge | Raphael Gottardo | Bayesian Robust Inference for Differential Gene Expression |
| CALIB | Hui Zhao | Calibration model for estimating absolute expression levels from microarray data |
| CAMERA | Carsten Kuhl | Collection of annotation related methods for mass spectrometry data |
| CGHbase | Sjoerd Vosse | CGHbase: Base functions and classes for arrayCGH data analysis. |
| CGHcall | Mark van de Wiel | Calling aberrations for array CGH tumor profiles. |
| cghMCR | J. Zhang | Find chromosome regions showing common gains/losses |
| CGHnormaliter | Bart P.P. van Houte | Normalization of array CGH data with imbalanced aberrations. |
| CGHregions | Sjoerd Vosse | Dimension Reduction for Array CGH Data with Minimal Information Loss. |
| charm | Martin Aryee | Analysis of DNA methylation data from CHARM microarrays |
| ChemmineR | ChemmineR Team | Analysis of Small Molecule and Screening Data |
| ChIPpeakAnno | Lihua Julie Zhu | Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. |
| chipseq | Biocore Team c/o BioC user list | chipseq: A package for analyzing chipseq data |
| ChIPseqR | Peter Humburg | Identifying Protein Binding Sites in High-Throughput Sequencing Data |
| ChIPsim | Peter Humburg | Simulation of ChIP-seq experiments |
| clippda | Stephen Nyangoma | A package for the clinical proteomic profiling data analysis |
| CNTools | J. Zhang | Convert segment data into a region by sample matrix to allow for other high level computational analyses. |
| codelink | Diego Diez | Manipulation of Codelink Bioarrays data. |
| CoGAPS | Elana J. Fertig , Michael F. Ochs | Coordinated Gene Activity in Pattern Sets |
| convert | Yee Hwa (Jean) Yang | Convert Microarray Data Objects |
| copa | James W. MacDonald | Functions to perform cancer outlier profile analysis. |
| CORREP | Dongxiao Zhu | Multivariate Correlation Estimator and Statistical Inference Procedures. |
| crlmm | Benilton S Carvalho , Robert Scharpf , Matt Ritchie | Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays. |
| CSAR | Jose M Muino | Statistical tools for the analysis of ChIP-seq data |
| ctc | Antoine Lucas | Cluster and Tree Conversion. |
| cycle | Matthias Futschik | Significance of periodic expression pattern in time-series data |
| daMA | Jobst Landgrebe | Efficient design and analysis of factorial two-colour microarray data |
| DEDS | Yuanyuan Xiao | Differential Expression via Distance Summary for Microarray Data |
| DEGraph | Laurent Jacob | Two-sample tests on a graph |
| DEGseq | Likun Wang | Identify Differentially Expressed Genes from RNA-seq data |
| DESeq | Simon Anders | Digital gene expresion analysis based on the negative binomial distribution |
| DFP | Rodrigo Alvarez-Glez | Gene Selection |
| diffGeneAnalysis | Choudary Jagarlamudi | Performs differential gene expression Analysis |
| DNAcopy | Venkatraman E. Seshan | DNA copy number data analysis |
| dualKS | Eric J. Kort | Dual KS Discriminant Analysis and Classification |
| dyebias | Philip Lijnzaad | The GASSCO method for correcting for slide-dependent gene-specific dye bias |
| edgeR | Mark Robinson , Davis McCarthy , Gordon Smyth | Empirical analysis of digital gene expression data in R |
| eisa | Gabor Csardi | Expression data analysis via the Iterative Signature Algorithm |
| exonmap | Crispin Miller | High level analysis of Affymetrix exon array data (DEPRECATED please use xmapcore) |
| explorase | Michael Lawrence | GUI for exploratory data analysis of systems biology data |
| ExpressionView | Gabor Csardi | Visualize biclusters identified in gene expression data |
| fabia | Sepp Hochreiter | FABIA: Factor Analysis for Bicluster Acquisition |
| factDesign | Denise Scholtens | Factorial designed microarray experiment analysis |
| farms | Djork-Arne Clevert | FARMS - Factor Analysis for Robust Microarray Summarization |
| fdrame | Effi Kenigsberg | FDR adjustments of Microarray Experiments (FDR-AME) |
| flagme | Mark Robinson | Analysis of Metabolomics GC/MS Data |
| flowClust | Raphael Gottardo | Clustering for Flow Cytometry |
| flowCore | F. Hahne | flowCore: Basic structures for flow cytometry data |
| flowFlowJo | John J. Gosink | Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm. |
| flowFP | Herb Holyst | Fingerprinting for Flow Cytometry |
| flowMeans | Nima Aghaeepour | Non-parametric Flow Cytometry Data Gating |
| flowMerge | Greg Finak | Cluster Merging for Flow Cytometry Data |
| flowQ | F. Hahne | Qualitiy control for flow cytometry |
| flowStats | Florian Hahne and Chao-Jen Wong | Statistical methods for the analysis of flow cytometry data |
| flowTrans | Greg Finak | Parameter Optimization for Flow Cytometry Data Transformation |
| flowUtils | Nishant Gopalakrishnan | Utilities for flow cytometry |
| flowViz | Florian Hahne | Visualization for flow cytometry |
| frma | Matthew N. McCall | Frozen RMA and Barcode |
| frmaTools | Matthew N. McCall | Frozen RMA Tools |
| gage | Weijun Luo | Generally Applicable Gene-set Enrichment for Pathway Analysis |
| gcrma | Z. Wu | Background Adjustment Using Sequence Information |
| genArise | IFC Development Team | Microarray Analysis tool |
| gene2pathway | Holger Froehlich | Prediction of KEGG pathway membership for individual genes based on InterPro domain signatures |
| genefilter | Biocore Team c/o BioC user list | genefilter: methods for filtering genes from microarray experiments |
| geneRecommender | Greg Hather | A gene recommender algorithm to identify genes coexpressed with a query set of genes |
| GeneRegionScan | Lasse Folkersen | GeneRegionScan |
| GeneTraffic | Daniel Iordan | GeneTraffic R Integration Functions |
| genoCN | Wei Sun | genotyping and copy number study tools |
| GenomeGraphs | Steffen Durinck | Plotting genomic information from Ensembl |
| GenomicFeatures | Biocore Team c/o BioC user list | Tools for making and manipulating transcript centric annotations |
| GenomicRanges | Biocore Team c/o BioC user list | Representation and manipulation of genomic intervals |
| GEOquery | Sean Davis | Get data from NCBI Gene Expression Omnibus (GEO) |
| GEOsubmission | Alexandre Kuhn | Prepares microarray data for submission to GEO |
| girafe | J. Toedling | Genome Intervals and Read Alignments for Functional Exploration |
| GLAD | Philippe Hupe | Gain and Loss Analysis of DNA |
| GlobalAncova | R. Meister | Calculates a global test for differential gene expression between groups |
| globaltest | Jelle Goeman | Testing groups of covariates/features for association with a response variable, with applications to gene set testing |
| goProfiles | Alex Sanchez | goProfiles: an R package for the statistical analysis of functional profiles |
| goseq | Matthew Young | Gene Ontology analyser for RNA-seq and other length biased data |
| goTools | Agnes Paquet | Functions for Gene Ontology database |
| gpls | Biocore Team c/o BioC user list | Classification using generalized partial least squares |
| GSEAlm | Assaf Oron | Linear Model Toolset for Gene Set Enrichment Analysis |
| GSRI | Julian Gehring | Gene Set Regulation Index |
| Harshlight | Maurizio Pellegrino | A "corrective make-up" program for microarray chips |
| Heatplus | Alexander Ploner | A heat map displaying covariates and coloring clusters |
| HELP | Reid F. Thompson | Tools for HELP data analysis |
| HEM | HyungJun Cho | Heterogeneous error model for identification of differentially expressed genes under multiple conditions |
| HTqPCR | Heidi Dvinge | Automated analysis of high-throughput qPCR data |
| iChip | Qianxing Mo | Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models |
| impute | Balasubramanian Narasimhan | impute: Imputation for microarray data |
| IsoGeneGUI | Setia Pramana | A graphical user interface to conduct a dose-response analysis of microarray data |
| ITALICS | Guillem Rigaill | ITALICS |
| iterativeBMA | Ka Yee Yeung | The Iterative Bayesian Model Averaging (BMA) algorithm |
| iterativeBMAsurv | Ka Yee Yeung | The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis |
| KCsmart | Jorma de Ronde | Multi sample aCGH analysis package using kernel convolution |
| lapmix | Yann Ruffieux | Laplace Mixture Model in Microarray Experiments |
| les | Julian Gehring | Identifying Loci of Enhanced Significance in Tiling Microarray Data |
| limma | Gordon Smyth | Linear Models for Microarray Data |
| limmaGUI | Keith Satterley | GUI for limma package |
| LMGene | Blythe Durbin-Johnson | LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays |
| logitT | Tobias Guennel | logit-t Package |
| LPE | Nitin Jain | Methods for analyzing microarray data using Local Pooled Error (LPE) method |
| LPEadj | Carl Murie | A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment with an unbiased adjustment based on sample size. |
| lumi | Pan Du | BeadArray Specific Methods for Illumina Methylation and Expression Microarrays |
| LVSmiRNA | Stefano Calza | LVS normalization for Agilent miRNA data |
| maanova | Keith Sheppard | Tools for analyzing Micro Array experiments |
| macat | Joern Toedling | MicroArray Chromosome Analysis Tool |
| maCorrPlot | Alexander Ploner | Visualize artificial correlation in microarray data |
| maDB | Johannes Rainer | Microarray database and utility functions for microarray data analysis. |
| maigesPack | Gustavo H. Esteves | Functions to handle cDNA microarray data, including several methods of data analysis |
| makecdfenv | James W. MacDonald | CDF Environment Maker |
| makePlatformDesign | Benilton Carvalho | Platform Design Package |
| MANOR | Pierre Neuvial | CGH Micro-Array NORmalization |
| marray | Yee Hwa (Jean) Yang | Exploratory analysis for two-color spotted microarray data |
| maSigPro | Ana Conesa | Significant Gene Expression Profile Differences in Time Course Microarray Data |
| MassArray | Reid F. Thompson | Analytical Tools for MassArray Data |
| MassSpecWavelet | Pan Du | Mass spectrum processing by wavelet-based algorithms |
| MBCB | Jeff Allen | MBCB (Model-based Background Correction for Beadarray) |
| mBPCR | P.M.V. Rancoita | Bayesian Piecewise Constant Regression for DNA copy number estimation |
| MEDIPS | Lukas Chavez | MeDIP-Seq data analysis |
| MEDME | Mattia Pelizzola | Modelling Experimental Data from MeDIP Enrichment |
| MergeMaid | Xiaogang Zhong | Merge Maid |
| metaArray | Hyungwon Choi | Integration of Microarray Data for Meta-analysis |
| metahdep | John R. Stevens | Hierarchical Dependence in Meta-Analysis |
| methylumi | Sean Davis | Handle Illumina methylation data |
| Mfuzz | Matthias Futschik | Soft clustering of time series gene expression data |
| MiChip | Jonathon Blake | MiChip Parsing and Summarizing Functions |
| minet | Patrick E. Meyer | Mutual Information NETworks |
| MiPP | Sukwoo Kim | Misclassification Penalized Posterior Classification |
| MotIV | Eloi Mercier , Raphael Gottardo | Motif Identification and Validation |
| Mulcom | Claudio Isella | Calculates MulCom test |
| multiscan | Mizanur Khondoker | R package for combining multiple scans |
| multtest | Katherine S. Pollard | Resampling-based multiple hypothesis testing |
| nem | Christian Bender | Nested Effects Models to reconstruct phenotypic hierarchies |
| netresponse | Leo Lahti | NetResponse: functional network analysis |
| nnNorm | Adi Laurentiu Tarca | Spatial and intensity based normalization of cDNA microarray data based on robust neural nets |
| nudge | N. Dean | Normal Uniform Differential Gene Expression detection |
| OCplus | Alexander Ploner | Operating characteristics plus sample size and local fdr for microarray experiments |
| oligo | Benilton Carvalho | Preprocessing tools for oligonucleotide arrays. |
| OLIN | Matthias Futschik | Optimized local intensity-dependent normalisation of two-color microarrays |
| OLINgui | Matthias Futschik | Graphical user interface for OLIN |
| oneChannelGUI | Raffaele A Calogero | This package extends the capabilities of affylmGUI graphical interface. Affymetrix 3' IVT, gene an exon arrays are actually implemented togheter with Illumina, GEO matrix series files and tab delimited files. Next Generation Sequencing secondary analysis for ncRNA quantification is also available. |
| OrderedList | Claudio Lottaz | Similarities of Ordered Gene Lists |
| OutlierD | Sukwoo Kim | Outlier detection using quantile regression on the M-A scatterplots of high-throughput data |
| pamr | Rob Tibshirani | Pam: prediction analysis for microarrays |
| pcot2 | Sarah Song | Principal Coordinates and Hotelling's T-Square method |
| PGSEA | Karl Dykema | Parametric Gene Set Enrichment Analysis |
| pickgene | Brian S. Yandell | Adaptive Gene Picking for Microarray Expression Data Analysis |
| PICS | Arnaud Droit , Xuekui Zhang , Raphael Gottardo | Probabilistic inference of ChIP-seq |
| pint | Olli-Pekka Huovilainen | Pairwise INTegration of functional genomics data |
| plateCore | Errol Strain | Statistical tools and data structures for plate-based flow cytometry |
| plgem | Norman Pavelka | Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM) |
| PLPE | Soo-heang Eo | Local Pooled Error Test for Differential Expression with Paired High-throughput Data |
| plw | Magnus Astrand | Probe level Locally moderated Weighted t-tests. |
| PROcess | Xiaochun Li | Ciphergen SELDI-TOF Processing |
| PROMISE | Xueyuan Cao | PRojection Onto the Most Interesting Statistical Evidence |
| puma | Richard Pearson , Li Zhang | Propagating Uncertainty in Microarray Analysis |
| qpgraph | Robert Castelo | Reverse engineering of molecular regulatory networks with qp-graphs |
| R453Plus1Toolbox | H-U Klein | A package for importing and analyzing data from Roche's Genome Sequencer System. |
| rama | Raphael Gottardo | Robust Analysis of MicroArrays |
| RBioinf | Robert Gentleman | RBioinf |
| rbsurv | Soo-heang Eo | Robust likelihood-based survival modeling with microarray data |
| Rdisop | Steffen Neumann | Decomposition of Isotopic Patterns |
| RDRToolbox | Christoph Bartenhagen | A package for nonlinear dimension reduction with Isomap and LLE. |
| reb | Karl J. Dykema | Regional Expression Biases |
| RefPlus | Kai-Ming Chang | A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods. |
| Resourcerer | Jianhua Zhang | Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge. |
| rGADEM | Arnaud Droit | de novo motif discovery |
| rHVDM | Martino Barenco | Hidden Variable Dynamic Modeling |
| Ringo | J. Toedling | R Investigation of ChIP-chip Oligoarrays |
| RLMM | Nusrat Rabbee | A Genotype Calling Algorithm for Affymetrix SNP Arrays |
| RMAGEML | Steffen Durinck | Handling MAGEML documents |
| Rmagpie | Camille Maumet | MicroArray Gene-expression-based Program In Error rate estimation |
| rMAT | Arnaud Droit and Raphael Gottardo | R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data. |
| RmiR | Francesco Favero | Package to work with miRNAs and miRNA targets with R |
| rnaSeqMap | Michal Okoniewski | rnaSeq analyses using xmapcore database |
| Rolexa | Jacques Rougemont | Statistical analysis of Solexa sequencing data |
| RPA | Leo Lahti | RPA: probe reliability and differential gene expression analysis |
| Rsamtools | Biocore Team c/o BioC user list | Import aligned BAM file format sequences into R / Bioconductor |
| RTools4TB | Aurelie Bergon | Data mining of public microarray data through connections to the TranscriptomeBrowser database. |
| sagenhaft | Tim Beissbarth | Collection of functions for reading and comparing SAGE libraries |
| SAGx | Per Broberg, | Statistical Analysis of the GeneChip |
| SamSPECTRAL | Habil Zare | Identifies cell population in flow cytometry data. |
| segmentSeq | Thomas J. Hardcastle | Methods for identifying small RNA loci from high-throughput sequencing data |
| ShortRead | Biocore Team c/o BioC user list | Classes and methods for high-throughput short-read sequencing data. |
| siggenes | Holger Schwender | Multiple testing using SAM and Efron's empirical Bayes approaches |
| SIM | Maarten van Iterson | Integrated Analysis on two human genomic datasets |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |
| simulatorAPMS | Tony Chiang | Computationally simulates the AP-MS technology. |
| sizepower | Weiliang Qiu | Sample Size and Power Calculation in Micorarray Studies |
| SMAP | Robin Andersson | A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling |
| snapCGH | John Marioni | Segmentation, normalisation and processing of aCGH data. |
| snpMatrix | David Clayton | The snp.matrix and X.snp.matrix classes |
| SpeCond | Florence Cavalli | Condition specific detection from expression data |
| SPIA | Adi Laurentiu Tarca | Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations |
| spikeLI | Enrico Carlon | Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool |
| spkTools | Matthew N McCall | Methods for Spike-in Arrays |
| splots | Wolfgang Huber | Visualization of high-throughput assays in microtitre plate or slide format |
| spotSegmentation | Chris Fraley | Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots |
| SRAdb | Jack Zhu | A compilation of metadata from NCBI SRA and tools |
| ssize | Gregory R. Warnes | Estimate Microarray Sample Size |
| SSPA | Maarten van Iterson | Sample Size and Power Analysis for Microarray Data |
| Starr | Benedikt Zacher | Simple tiling array analysis of Affymetrix ChIP-chip data |
| stepNorm | Yuanyuan Xiao | Stepwise normalization functions for cDNA microarrays |
| TargetSearch | Alvaro Cuadros-Inostroza | A package for the analysis of GC-MS metabolite profiling data. |
| tigre | Antti Honkela | Transcription factor Inference through Gaussian process Reconstruction of Expression |
| tilingArray | Zhenyu Xu | Transcript mapping with high-density oligonucleotide tiling arrays |
| timecourse | Yu Chuan Tai | Statistical Analysis for Developmental Microarray Time Course Data |
| topGO | Adrian Alexa | topGO: Enrichment analysis for Gene Ontology |
| tspair | Jeffrey T. Leek | Top Scoring Pairs for Microarray Classification |
| twilight | Stefanie Scheid | Estimation of local false discovery rate |
| vsn | Wolfgang Huber | Variance stabilization and calibration for microarray data |
| webbioc | Colin A. Smith | Bioconductor Web Interface |
| xcms | Colin A. Smith | LC/MS and GC/MS Data Analysis |
| XDE | Robert Scharpf | XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression |
| xmapcore | Tim Yates | Core access to the xmap database (installed separately) |
| xps | Christian Stratowa | Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays |
| yaqcaffy | Laurent Gatto | Affymetrix expression data quality control and reproducibility analysis |