| Package | Maintainer | Title |
|---|---|---|
| aCGH | Peter Dimitrov | Classes and functions for Array Comparative Genomic Hybridization data. |
| Biostrings | H. Pages | String objects representing biological sequences, and matching algorithms |
| BSgenome | H. Pages | Infrastructure for Biostrings-based genome data packages |
| ChemmineR | ChemmineR Team | Analysis of Small Molecule and Screening Data |
| clippda | Stephen Nyangoma | A package for the clinical proteomic profiling data analysis |
| CRImage | Henrik Failmezger , Yinyin Yuan | CRImage a package to classify cells and calculate tumour cellularity |
| CSAR | Jose M Muino | Statistical tools for the analysis of ChIP-seq data |
| flowMeans | Nima Aghaeepour | Non-parametric Flow Cytometry Data Gating |
| gage | Weijun Luo | Generally Applicable Gene-set Enrichment for Pathway Analysis |
| GeneR | Y. d'Aubenton-Carafa | R for genes and sequences analysis |
| GeneRfold | Antoine Lucas | R for genes and sequences, using viennaRNA package (fold) |
| GeneticsDesign | The R Genetics Project | Functions for designing genetics studies |
| GeneticsPed | David Henderson | Pedigree and genetic relationship functions |
| genoCN | Wei Sun | genotyping and copy number study tools |
| genomeIntervals | Julien Gagneur | Operations on genomic intervals |
| genomes | Chris Stubben | Genome sequencing project metadata |
| 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 |
| GGBase | Vince Carey | infrastructure for genetics of gene expression (c) 2008 VJ Carey |
| GGtools | Vince Carey | software and data for genetics of gene expression (c) 2006 VJ Carey |
| GSRI | Julian Gehring | Gene Set Regulation Index |
| IPPD | Martin Slawski | Isotopic peak pattern deconvolution for Protein Mass Spectrometry by template matching |
| LiquidAssociation | Yen-Yi Ho | LiquidAssociation |
| logicFS | Holger Schwender | Identification of SNP Interactions |
| 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. |
| MassArray | Reid F. Thompson | Analytical Tools for MassArray Data |
| MassSpecWavelet | Pan Du | Mass spectrum processing by wavelet-based algorithms |
| MLP | Tobias Verbeke | MLP |
| mosaics | Dongjun Chung | MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq) |
| MSnbase | Laurent Gatto | MSnbase: Base Functions and Classes for MS-based Proteomics |
| netresponse | Leo Lahti | NetResponse: functional network analysis |
| NuPoP | Ji-Ping Wang | An R package for nucleosome positioning prediction |
| PAnnBuilder | Li Hong | Protein annotation data package builder |
| PCpheno | Nolwenn Le Meur | Phenotypes and cellular organizational units |
| pint | Olli-Pekka Huovilainen | Pairwise INTegration of functional genomics data |
| 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 |
| ppiStats | Tony Chiang | Protein-Protein Interaction Statistical Package |
| PROcess | Xiaochun Li | Ciphergen SELDI-TOF Processing |
| procoil | Ulrich Bodenhofer | Prediction of Oligomerization of Coiled Coil Proteins |
| RMAPPER | Heike Sichtig , Alberto Riva | R interface to the MAPPER database of transcription factor binding sites |
| RpsiXML | Jitao David Zhang | R interface to PSI-MI 2.5 files |
| SamSPECTRAL | Habil Zare | Identifies cell population in flow cytometry data. |
| ScISI | Tony Chiang | In Silico Interactome |
| SLGI | Nolwenn Le Meur | Synthetic Lethal Genetic Interaction |
| TEQC | Manuela Hummel | Quality control for target capture experiments |