| Package | Maintainer | Title |
|---|---|---|
| aCGH | Peter Dimitrov | Classes and functions for Array Comparative Genomic Hybridization data. |
| affxparser | Kasper Daniel Hansen | Affymetrix File Parsing SDK |
| AffyCompatible | Martin Morgan | Affymetrix GeneChip software compatibility |
| affyContam | V. Carey | structured corruption of affymetrix cel file data |
| AffyExpress | Xuejun Arthur Li | Affymetrix Quality Assessment and Analysis Tool |
| affyio | Benjamin Milo Bolstad | Tools for parsing Affymetrix data files |
| affylmGUI | Keith Satterley | GUI for affy analysis using limma package |
| AnnotationDbi | Biocore Team c/o BioC user list | Annotation Database Interface |
| apComplex | Denise Scholtens | Estimate protein complex membership using AP-MS protein data |
| aroma.light | Henrik Bengtsson | Light-weight methods for normalization and visualization of microarray data using only basic R data types |
| ArrayExpress | Audrey Kauffmann | Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet |
| arrayMvout | V. Carey | multivariate outlier detection for expression array QA |
| arrayQuality | Agnes Paquet | Assessing array quality on spotted arrays |
| ArrayTools | Arthur Li | geneChip Analysis Package |
| beadarraySNP | Jan Oosting | Normalization and reporting of Illumina SNP bead arrays |
| Biobase | Biocore Team c/o BioC user list | Biobase: Base functions for Bioconductor |
| BiocCaseStudies | Biocore Team c/o BioC user list | BiocCaseStudies: Support for the Case Studies Monograph |
| biocDatasets | L. Gautier | Synthetic datasets for bioconductor |
| biocGraph | Florian Hahne | Graph examples and use cases in Bioinformatics |
| biocViews | Biocore Team c/o BioC user list | Categorized views of R package repositories |
| BioMVCClass | Elizabeth Whalen | Model-View-Controller (MVC) Classes That Use Biobase |
| BioNet | Marcus Dittrich | Routines for the functional analysis of biological networks |
| Biostrings | H. Pages | String objects representing biological sequences, and matching algorithms |
| BSgenome | H. Pages | Infrastructure for Biostrings-based genome data packages |
| BufferedMatrix | Benjamin Milo Bolstad | A matrix data storage object held in temporary files |
| BufferedMatrixMethods | B. M. Bolstad | Microarray Data related methods that utlize BufferedMatrix objects |
| cellHTS | Ligia Bras | Analysis of cell-based screens |
| cellHTS2 | Florian Hahne | Analysis of cell-based screens - revised version of cellHTS |
| CGHbase | Sjoerd Vosse | CGHbase: Base functions and classes for arrayCGH data analysis. |
| CGHcall | Mark van de Wiel | Calling aberrations for array CGH tumor profiles. |
| CGHregions | Sjoerd Vosse | Dimension Reduction for Array CGH Data with Minimal Information Loss. |
| ChemmineR | ChemmineR Team | Analysis of Small Molecule and Screening Data |
| ChIPseqR | Peter Humburg | Identifying Protein Binding Sites in High-Throughput Sequencing Data |
| ChIPsim | Peter Humburg | Simulation of ChIP-seq experiments |
| ChromHeatMap | Tim F. Rayner | Heat map plotting by genome coordinate |
| clstutils | Noah Hoffman | Tools for performing taxonomic assignment. |
| clusterProfiler | Guangchuang Yu | statistical analysis and visulization of functional profiles for genes and gene clusters |
| codelink | Diego Diez | Manipulation of Codelink Bioarrays data. |
| convert | Yee Hwa (Jean) Yang | Convert Microarray Data Objects |
| copa | James W. MacDonald | Functions to perform cancer outlier profile analysis. |
| CORREP | Dongxiao Zhu | Multivariate Correlation Estimator and Statistical Inference Procedures. |
| cosmoGUI | Oliver Bembom | GUI for constructing constraint sets used by the cosmo package |
| ctc | Antoine Lucas | Cluster and Tree Conversion. |
| DEGraph | Laurent Jacob | Two-sample tests on a graph |
| DynDoc | Biocore Team c/o BioC user list | Dynamic document tools |
| EBImage | Gregoire Pau | Image processing toolbox for R |
| ecolitk | Laurent Gautier | Meta-data and tools for E. coli |
| eisa | Gabor Csardi | Expression data analysis via the Iterative Signature Algorithm |
| exonmap | Crispin Miller | High level analysis of Affymetrix exon array data (DEPRECATED please use xmapcore) |
| explorase | Michael Lawrence | GUI for exploratory data analysis of systems biology data |
| ExpressionView | Gabor Csardi | Visualize biclusters identified in gene expression data |
| externalVector | Biocore Team c/o BioC user list | Vector objects for R with external storage |
| fabia | Sepp Hochreiter | FABIA: Factor Analysis for Bicluster Acquisition |
| flowClust | Raphael Gottardo | Clustering for Flow Cytometry |
| flowCore | F. Hahne | flowCore: Basic structures for flow cytometry data |
| flowFP | Herb Holyst | Fingerprinting for Flow Cytometry |
| flowPhyto | David M. Schruth | Methods for Continuous Flow Cytometry |
| flowPlots | N. Hawkins | flowPlots: analysis plots and data class for gated flow cytometry data |
| flowQ | F. Hahne | Quality control for flow cytometry |
| flowUtils | Nishant Gopalakrishnan | Utilities for flow cytometry |
| flowViz | Florian Hahne | Visualization for flow cytometry |
| gage | Weijun Luo | Generally Applicable Gene-set Enrichment for Pathway Analysis |
| gaggle | Christopher Bare | Broadcast data between R and Gaggle |
| gene2pathway | Holger Froehlich | Prediction of KEGG pathway membership for individual genes based on InterPro domain signatures |
| GeneAnswers | Gang Feng and Pan Du | Integrated Interpretation of Genes |
| geneplotter | Biocore Team c/o BioC user list | Graphics related functions for Bioconductor |
| GeneRegionScan | Lasse Folkersen | GeneRegionScan |
| GeneSpring | Thon de Boer | GeneSpring R Integration Functions |
| GeneTraffic | Daniel Iordan | GeneTraffic R Integration Functions |
| GenomeGraphs | Steffen Durinck | Plotting genomic information from Ensembl |
| genomeIntervals | Julien Gagneur | Operations on genomic intervals |
| GenomicFeatures | Biocore Team c/o BioC user list | Tools for making and manipulating transcript centric annotations |
| Genominator | James Bullard | Analyze, manage and store genomic data |
| GEOmetadb | Jack Zhu | A compilation of metadata from NCBI GEO |
| GEOquery | Sean Davis | Get data from NCBI Gene Expression Omnibus (GEO) |
| goTools | Agnes Paquet | Functions for Gene Ontology database |
| graph | Seth Falcon | graph: A package to handle graph data structures |
| GraphAlignment | Joern P. Meier | GraphAlignment |
| GraphAT | Thomas LaFramboise | Graph Theoretic Association Tests |
| GSEABase | Biocore Team c/o BioC user list | Gene set enrichment data structures and methods |
| Heatplus | Alexander Ploner | A heat map displaying covariates and coloring clusters |
| HELP | Reid F. Thompson | Tools for HELP data analysis |
| HilbertVis | Simon Anders | Hilbert curve visualization |
| HilbertVisGUI | Simon Anders | HilbertVisGUI |
| HTqPCR | Heidi Dvinge | Automated analysis of high-throughput qPCR data |
| hyperdraw | Paul Murrell | Visualizing Hypergaphs |
| hypergraph | Biocore Team c/o BioC user list | A package providing hypergraph data structures |
| ibh | Kircicegi Korkmaz | Interaction Based Homogeneity for Evaluating Gene Lists |
| Icens | Biocore Team c/o BioC user list | NPMLE for Censored and Truncated Data |
| idiogram | Karl J. Dykema | idiogram |
| iFlow | Kyongryun Lee | GUI based visualization for flow cytometry |
| imageHTS | Gregoire Pau | Analysis of high-throughput microscopy-based screens |
| IRanges | Biocore Team c/o BioC user list | Infrastructure for manipulating intervals on sequences |
| IsoGeneGUI | Setia Pramana | A graphical user interface to conduct a dose-response analysis of microarray data |
| KCsmart | Jorma de Ronde | Multi sample aCGH analysis package using kernel convolution |
| KEGGgraph | Jitao David Zhang | KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor |
| keggorthology | VJ Carey | graph support for KO, KEGG Orthology |
| limma | Gordon Smyth | Linear Models for Microarray Data |
| limmaGUI | Keith Satterley | GUI for limma package |
| macat | Joern Toedling | MicroArray Chromosome Analysis Tool |
| maCorrPlot | Alexander Ploner | Visualize artificial correlation in microarray data |
| maDB | Johannes Rainer | Microarray database and utility functions for microarray data analysis. |
| maigesPack | Gustavo H. Esteves | Functions to handle cDNA microarray data, including several methods of data analysis |
| makecdfenv | James W. MacDonald | CDF Environment Maker |
| makePlatformDesign | Benilton Carvalho | Platform Design Package |
| MANOR | Pierre Neuvial | CGH Micro-Array NORmalization |
| MassArray | Reid F. Thompson | Analytical Tools for MassArray Data |
| mcaGUI | Wade K. Copeland | Microbial Community Analysis GUI |
| MEDIPS | Lukas Chavez | MeDIP-Seq data analysis |
| MergeMaid | Xiaogang Zhong | Merge Maid |
| Mfuzz | Matthias Futschik | Soft clustering of time series gene expression data |
| microRNA | Chao-Jen Wong | Data and functions for dealing with microRNAs |
| minet | Patrick E. Meyer | Mutual Information NETworks |
| MSnbase | Laurent Gatto | MSnbase: Base Functions and Classes for MS-based Proteomics |
| MVCClass | Elizabeth Whalen | Model-View-Controller (MVC) Classes |
| nem | Christian Bender | Nested Effects Models to reconstruct phenotypic hierarchies |
| netresponse | Leo Lahti | NetResponse: functional network analysis |
| NuPoP | Ji-Ping Wang | An R package for nucleosome positioning prediction |
| oligo | Benilton Carvalho | Preprocessing tools for oligonucleotide arrays. |
| oligoClasses | Benilton Carvalho and Robert Scharpf | Classes for high-throughput arrays supported by oligo and crlmm |
| OLIN | Matthias Futschik | Optimized local intensity-dependent normalisation of two-color microarrays |
| OLINgui | Matthias Futschik | Graphical user interface for OLIN |
| 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. |
| ontoCAT | Natalja Kurbatova | Ontology traversal and search |
| ontoTools | Vince Carey | graphs and sparse matrices for working with ontologies; formal objects for nomenclatures with provenance management |
| OTUbase | Daniel Beck | Provides structure and functions for the analysis of OTU data |
| panp | Peter Warren | Presence-Absence Calls from Negative Strand Matching Probesets |
| pathRender | Li Long | Render molecular pathways |
| PCpheno | Nolwenn Le Meur | Phenotypes and cellular organizational units |
| pdInfoBuilder | Benilton Carvalho | Platform Design Information Package Builder |
| pgUtils | Johannes Rainer | Utility functions for PostgreSQL databases |
| PICS | Arnaud Droit , Xuekui Zhang , Raphael Gottardo | Probabilistic inference of ChIP-seq |
| pkgDepTools | Seth Falcon | Package Dependency Tools |
| plateCore | Errol Strain | Statistical tools and data structures for plate-based flow cytometry |
| ppiStats | Tony Chiang | Protein-Protein Interaction Statistical Package |
| prada | Florian Hahne | Data analysis for cell-based functional assays |
| preprocessCore | Benjamin Milo Bolstad | A collection of pre-processing functions |
| qpgraph | Robert Castelo | Reverse engineering of molecular regulatory networks with qp-graphs |
| quantsmooth | Jan Oosting | Quantile smoothing and genomic visualization of array data |
| R453Plus1Toolbox | Hans-Ulrich Klein | A package for importing and analyzing data from Roche's Genome Sequencer System. |
| RBGL | Li Long | An interface to the BOOST graph library |
| RCytoscape | Paul Shannon | Display and manipulate graphs in Cytoscape |
| Rdbi | Jianhua Zhang | Generic database methods |
| RdbiPgSQL | Jianhua Zhang | PostgreSQL access |
| RDRToolbox | Christoph Bartenhagen | A package for nonlinear dimension reduction with Isomap and LLE. |
| reb | Karl J. Dykema | Regional Expression Biases |
| rflowcyt | N. LeMeur | Statistical tools and data structures for analytic flow cytometry |
| Rgraphviz | Kasper Hansen | Provides plotting capabilities for R graph objects |
| rHVDM | Martino Barenco | Hidden Variable Dynamic Modeling |
| Ringo | J. Toedling | R Investigation of ChIP-chip Oligoarrays |
| RmiR | Francesco Favero | Package to work with miRNAs and miRNA targets with R |
| RNAinteract | Bernd Fischer | Estimate Pairwise Interactions from multidimensional features |
| RNAither | Nora Rieber | Statistical analysis of high-throughput RNAi screens |
| rnaSeqMap | Michal Okoniewski | rnaSeq analyses using xmapcore database |
| Rolexa | Jacques Rougemont | Statistical analysis of Solexa sequencing data |
| RpsiXML | Jitao David Zhang | R interface to PSI-MI 2.5 files |
| Rredland | VJ Carey | interface to redland RDF utilities |
| Rsamtools | Biocore Team c/o BioC user list | Import aligned BAM file format sequences into R / Bioconductor |
| rsbml | Michael Lawrence | R support for SBML, using libsbml |
| RTCA | Jitao David Zhang | Open-source toolkit to analyse data from xCELLigence System (RTCA) by Roche |
| 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 |
| Ruuid | Biocore Team c/o BioC user list | Ruuid: Provides Universally Unique ID values |
| RWebServices | Martin Morgan | Expose R functions as web services through Java/Axis/Apache |
| SAGx | Per Broberg, | Statistical Analysis of the GeneChip |
| SBMLR | Tomas Radivoyevitch | SBML-R Interface and Analysis Tools |
| ScISI | Tony Chiang | In Silico Interactome |
| ShortRead | Biocore Team c/o BioC user list | Classes and methods for high-throughput short-read sequencing data. |
| SIM | Maarten van Iterson | Integrated Analysis on two human genomic datasets |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |
| simulatorAPMS | Tony Chiang | Computationally simulates the AP-MS technology. |
| SJava | Martin Morgan | The Omegahat interface for R and Java. |
| SLGI | Nolwenn Le Meur | Synthetic Lethal Genetic Interaction |
| SNPchip | Robert Scharpf | Classes and Methods for high throughput SNP chip data |
| SPIA | Adi Laurentiu Tarca | Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations |
| splicegear | Laurent Gautier | splicegear |
| splots | Wolfgang Huber | Visualization of high-throughput assays in microtitre plate or slide format |
| SQUADD | Martial Sankar | Add-on of the SQUAD Software |
| SRAdb | Jack Zhu | A compilation of metadata from NCBI SRA and tools |
| Starr | Benedikt Zacher | Simple tiling array analysis of Affymetrix ChIP-chip data |
| tilingArray | Zhenyu Xu | Transcript mapping with high-density oligonucleotide tiling arrays |
| tkWidgets | J. Zhang | R based tk widgets |
| topGO | Adrian Alexa | topGO: Enrichment analysis for Gene Ontology |
| TypeInfo | Duncan Temple Lang | Optional Type Specification Prototype |
| VanillaICE | Robert Scharpf | A Hidden Markov Model for high throughput genotyping arrays |
| weaver | Seth Falcon | Tools and extensions for processing Sweave documents |
| webbioc | Colin A. Smith | Bioconductor Web Interface |
| widgetTools | Jianhua Zhang | Creates an interactive tcltk widget |
| xmapbridge | Tim Yates | Export plotting files to the xmapBridge for visualisation in X:Map |
| xmapcore | Tim Yates | Core access to the xmap database (installed separately) |
| xps | Christian Stratowa | Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays |