| Package | Maintainer | Title |
|---|---|---|
| AffyExpress | Xuejun Arthur Li | Affymetrix Quality Assessment and Analysis Tool |
| 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 |
| arrayQuality | Agnes Paquet | Assessing array quality on spotted arrays |
| ArrayTools | Arthur Li | geneChip Analysis Package |
| BioMVCClass | Elizabeth Whalen | Model-View-Controller (MVC) Classes That Use Biobase |
| BioNet | Marcus Dittrich | Routines for the functional analysis of biological networks |
| cellHTS | Ligia Bras | Analysis of cell-based screens |
| cellHTS2 | Florian Hahne | Analysis of cell-based screens - revised version of cellHTS |
| 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 |
| 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 |
| copa | James W. MacDonald | Functions to perform cancer outlier profile analysis. |
| ctc | Antoine Lucas | Cluster and Tree Conversion. |
| 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 |
| fabia | Sepp Hochreiter | FABIA: Factor Analysis for Bicluster Acquisition |
| flowClust | Raphael Gottardo | Clustering for Flow Cytometry |
| 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 |
| flowViz | Florian Hahne | Visualization for flow cytometry |
| gaggle | Christopher Bare | Broadcast data between R and Gaggle |
| 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 |
| GenomeGraphs | Steffen Durinck | Plotting genomic information from Ensembl |
| goTools | Agnes Paquet | Functions for Gene Ontology database |
| 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 |
| idiogram | Karl J. Dykema | idiogram |
| imageHTS | Gregoire Pau | Analysis of high-throughput microscopy-based screens |
| KCsmart | Jorma de Ronde | Multi sample aCGH analysis package using kernel convolution |
| 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. |
| 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 |
| MVCClass | Elizabeth Whalen | Model-View-Controller (MVC) Classes |
| NuPoP | Ji-Ping Wang | An R package for nucleosome positioning prediction |
| OLIN | Matthias Futschik | Optimized local intensity-dependent normalisation of two-color microarrays |
| OLINgui | Matthias Futschik | Graphical user interface for OLIN |
| PICS | Arnaud Droit , Xuekui Zhang , Raphael Gottardo | Probabilistic inference of ChIP-seq |
| prada | Florian Hahne | Data analysis for cell-based functional assays |
| 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. |
| RDRToolbox | Christoph Bartenhagen | A package for nonlinear dimension reduction with Isomap and LLE. |
| reb | Karl J. Dykema | Regional Expression Biases |
| 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 |
| RTCA | Jitao David Zhang | Open-source toolkit to analyse data from xCELLigence System (RTCA) by Roche |
| rtracklayer | Michael Lawrence | R interface to genome browsers and their annotation tracks |
| SIM | Maarten van Iterson | Integrated Analysis on two human genomic datasets |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |
| SNPchip | Robert Scharpf | Classes and Methods for high throughput SNP chip data |
| splots | Wolfgang Huber | Visualization of high-throughput assays in microtitre plate or slide format |
| tilingArray | Zhenyu Xu | Transcript mapping with high-density oligonucleotide tiling arrays |
| topGO | Adrian Alexa | topGO: Enrichment analysis for Gene Ontology |
| VanillaICE | Robert Scharpf | A Hidden Markov Model for high throughput genotyping arrays |
| 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) |