| Package | Maintainer | Title |
|---|---|---|
| Biostrings | H. Pages | String objects representing biological sequences, and matching algorithms |
| 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 |
| mcaGUI | Wade K. Copeland | Microbial Community Analysis GUI |
| MEDIPS | Lukas Chavez | MeDIP-Seq data analysis |
| mosaics | Dongjun Chung | MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq) |
| PICS | Arnaud Droit , Xuekui Zhang , Raphael Gottardo | Probabilistic inference of ChIP-seq |
| rGADEM | Arnaud Droit | de novo motif discovery |
| 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 |
| Rsubread | Wei Shi | Rsubread: a super fast, sensitive and accurate read aligner for mapping next-generation sequencing reads |
| 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. |