| 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 |
| clstutils | Noah Hoffman | Tools for performing taxonomic assignment. |
| 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 |
| MEDIPS | Lukas Chavez | MeDIP-Seq data analysis |
| mosaics | Dongjun Chung | MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq) |
| 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 | Hans-Ulrich 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 |
| Rsubread | Wei Shi | Rsubread: a super fast, sensitive and accurate read aligner for mapping next-generation sequencing reads |
| segmentSeq | Thomas J. Hardcastle | Methods for identifying small RNA loci from high-throughput sequencing data |
| seqbias | Daniel Jones | Estimation of per-position bias in 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 |
| TEQC | Manuela Hummel | Quality control for target capture experiments |