| Package | Maintainer | Title |
|---|---|---|
| BayesPeak | Jonathan Cairns | Bayesian Analysis of ChIP-seq Data |
| baySeq | Thomas J. Hardcastle | Empirical Bayesian analysis of patterns of differential expression in count 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 |
| CSAR | Jose M Muino | Statistical tools for the analysis of ChIP-seq data |
| DEGseq | Likun Wang | Identify Differentially Expressed Genes from RNA-seq data |
| DESeq | Simon Anders | Digital gene expresion analysis based on the negative binomial distribution |
| edgeR | Mark Robinson , Davis McCarthy , Gordon Smyth | Empirical analysis of digital gene expression data in R |
| gage | Weijun Luo | Generally Applicable Gene-set Enrichment for Pathway Analysis |
| 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 |
| girafe | J. Toedling | Genome Intervals and Read Alignments for Functional Exploration |
| goseq | Matthew Young | Gene Ontology analyser for RNA-seq and other length biased data |
| MotIV | Eloi Mercier , Raphael Gottardo | Motif Identification and Validation |
| 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. |
| PICS | Arnaud Droit , Xuekui Zhang , Raphael Gottardo | Probabilistic inference of ChIP-seq |
| R453Plus1Toolbox | H-U Klein | A package for importing and analyzing data from Roche's Genome Sequencer System. |
| rGADEM | Arnaud Droit | de novo motif discovery |
| rnaSeqMap | Michal Okoniewski | rnaSeq analyses using xmapcore database |
| Rsamtools | Biocore Team c/o BioC user list | Import aligned BAM file format sequences into R / Bioconductor |
| 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. |
| splots | Wolfgang Huber | Visualization of high-throughput assays in microtitre plate or slide format |
| SRAdb | Jack Zhu | A compilation of metadata from NCBI SRA and tools |