Package |
Maintainer |
Title |
aCGH
|
Peter Dimitrov |
Classes and functions for Array Comparative Genomic
Hybridization data. |
affxparser
|
Kasper Daniel Hansen |
Affymetrix File Parsing SDK |
affyio
|
Benjamin Milo Bolstad |
Tools for parsing Affymetrix data files |
affylmGUI
|
Keith Satterley |
GUI for affy analysis using limma package |
ArrayExpress
|
Audrey Kauffmann |
Access the ArrayExpress Microarray Database at EBI and build
Bioconductor data structures: ExpressionSet, AffyBatch,
NChannelSet |
beadarraySNP
|
Jan Oosting |
Normalization and reporting of Illumina SNP bead arrays |
BioNet
|
Marcus Dittrich
|
Routines for the functional analysis of biological networks |
Biostrings
|
H. Pages |
String objects representing biological sequences, and matching
algorithms |
ChemmineR
|
ChemmineR Team |
Analysis of Small Molecule and Screening Data |
codelink
|
Diego Diez |
Manipulation of Codelink Bioarrays data. |
ctc
|
Antoine Lucas |
Cluster and Tree Conversion. |
exonmap
|
Crispin Miller |
High level analysis of Affymetrix exon array data (DEPRECATED
please use xmapcore) |
flowPhyto
|
David M. Schruth |
Methods for Continuous Flow Cytometry |
gaggle
|
Christopher Bare |
Broadcast data between R and Gaggle |
GeneRegionScan
|
Lasse Folkersen |
GeneRegionScan |
genomeIntervals
|
Julien Gagneur |
Operations on genomic intervals |
GEOquery
|
Sean Davis |
Get data from NCBI Gene Expression Omnibus (GEO) |
HELP
|
Reid F. Thompson |
Tools for HELP data analysis |
HTqPCR
|
Heidi Dvinge |
Automated analysis of high-throughput qPCR data |
ibh
|
Kircicegi Korkmaz |
Interaction Based Homogeneity for Evaluating Gene Lists |
limma
|
Gordon Smyth |
Linear Models for Microarray Data |
limmaGUI
|
Keith Satterley |
GUI for limma package |
makecdfenv
|
James W. MacDonald |
CDF Environment Maker |
MANOR
|
Pierre Neuvial |
CGH Micro-Array NORmalization |
MassArray
|
Reid F. Thompson |
Analytical Tools for MassArray Data |
oligo
|
Benilton Carvalho |
Preprocessing tools for oligonucleotide arrays. |
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. |
OTUbase
|
Daniel Beck |
Provides structure and functions for the analysis of OTU data |
R453Plus1Toolbox
|
Hans-Ulrich Klein |
A package for importing and analyzing data from Roche's Genome
Sequencer System. |
Ringo
|
J. Toedling |
R Investigation of ChIP-chip Oligoarrays |
Rolexa
|
Jacques Rougemont |
Statistical analysis of Solexa sequencing data |
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. |
rtracklayer
|
Michael Lawrence |
R interface to genome browsers and their annotation tracks |
SAGx
|
Per Broberg, |
Statistical Analysis of the GeneChip |
ShortRead
|
Biocore Team c/o BioC user list
|
Classes and methods for high-throughput short-read sequencing
data. |
simpleaffy
|
Crispin Miller |
Very simple high level analysis of Affymetrix data |
SRAdb
|
Jack Zhu |
A compilation of metadata from NCBI SRA and tools |
Starr
|
Benedikt Zacher |
Simple tiling array analysis of Affymetrix ChIP-chip data |
xps
|
Christian Stratowa |
Processing and Analysis of Affymetrix Oligonucleotide Arrays
including Exon Arrays, Whole Genome Arrays and Plate Arrays |