| Package | Maintainer | Title |
|---|---|---|
| ABarray | Yongming Andrew Sun | Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Micorarray (AB1700) gene expression data. |
| aCGH | Jane Fridlyand | Classes and functions for Array Comparative Genomic Hybridization data. |
| affxparser | Kasper Daniel Hansen | Affymetrix File Parsing SDK |
| affy | Rafael A. Irizarry | Methods for Affymetrix Oligonucleotide Arrays |
| affycomp | Rafael A. Irizarry | Graphics Toolbox for Assessment of Affymetrix Expression Measures |
| AffyCompatible | Martin Morgan | Affymetrix GeneChip software compatibility |
| affyContam | V. Carey | structured corruption of affymetrix cel file data |
| affycoretools | James W. MacDonald | Functions useful for those doing repetitive analyses with Affymetrix GeneChips. |
| 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 |
| affyPara | Markus Schmidberger | Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays |
| affypdnn | Laurent Gautier | Probe Dependent Nearest Neighbours (PDNN) for the affy package |
| affyPLM | Ben Bolstad | Methods for fitting probe-level models |
| affyQCReport | Craig Parman | QC Report Generation for affyBatch objects |
| Agi4x44PreProcess | Pedro Lopez-Romero | PreProcessing of Agilent 4x44 array data |
| altcdfenvs | Laurent Gautier | alternative CDF environments (aka mappings) |
| 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 |
| arrayQualityMetrics | Audrey Kauffmann | Quality metrics on microarray data sets |
| ArrayTools | Arthur Li | geneChip Analysis Package |
| beadarray | Mark Dunning | Quality assessment and low-level analysis for Illumina BeadArray data |
| 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 |
| biocGraph | Li Long | 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 |
| 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 |
| CALIB | Hui Zhao | Calibration model for estimating absolute expression levels from microarray data |
| 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 | Sjoerd Vosse | Calling aberrations for array CGH tumor profiles. |
| CGHregions | Sjoerd Vosse | Dimension Reduction for Array CGH Data with Minimal Information Loss. |
| 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. |
| DynDoc | Biocore Team c/o BioC user list | Dynamic document tools |
| EBImage | Gregoire Pau | Image processing and image analysis toolkit for R |
| ecolitk | Laurent | Meta-data and tools for E. coli |
| exonmap | Crispin Miller | High level analysis of Affymetrix exon array data |
| explorase | Michael Lawrence | GUI for exploratory data analysis of systems biology data |
| externalVector | Biocore Team c/o BioC user list | Vector objects for R with external storage |
| flowClust | Raphael Gottardo | Clustering for Flow Cytometry |
| flowCore | Nolwenn Le Meur | flowCore: Basic structures for flow cytometry data |
| flowQ | N. Le Meur | Qualitiy control for flow cytometry |
| flowUtils | Nishant Gopalakrishnan | Utilities for flow cytometry |
| flowViz | Florian Hahne | Visualization for flow cytometry |
| gaggle | Dan Tenenbaum | Broadcast data between R and other bioinformatics programs |
| gcrma | Z. Wu | Background Adjustment Using Sequence Information |
| genArise | IFC Development Team | Microarray Analysis tool |
| geneplotter | Biocore Team c/o BioC user list | Grapics related functions for Bioconductor |
| GeneSpring | Thon de Boer | GeneSpring R Integration Functions |
| GeneTraffic | Daniel Iordan | GeneTraffic R Integration Functions |
| GenomeGraphs | Steffen Durinck | Plotting genomic information from Ensembl |
| 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 | Robert Gentleman | 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 |
| hexbin | Nicholas Lewin-Koh | Hexagonal Binning Routines |
| HilbertVis | Simon Anders | Hilbert curve visualization |
| HilbertVisGUI | Simon Anders | HilbertVisGUI |
| hypergraph | Robert Gentleman | A package providing hypergraph data structures |
| Icens | Biocore Team c/o BioC user list | NPMLE for Censored and Truncated Data |
| idiogram | Karl J. Dykema | idiogram |
| IRanges | Biocore Team c/o BioC user list | Low-level containers for storing sets of integer ranges |
| KCsmart | Jorma de Ronde | Multi sample aCGH analysis package using kernel convolution |
| limma | Gordon Smyth | Linear Models for Microarray Data |
| limmaGUI | Keith Satterley | GUI for limma package |
| LMGene | John Tillinghast | LMGene Software for Date Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays |
| lumi | Pan Du | BeadArray Specific Methods for Illumina Microarrays |
| 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 |
| marray | Yee Hwa (Jean) Yang | Exploratory analysis for two-color spotted microarray data |
| MergeMaid | Xiaogang Zhong | Merge Maid |
| microRNA | Robert Gentleman | Data and functions for dealing with microRNAs |
| minet | Patrick E. Meyer | Mutual Information Network Inference |
| multiscan | Mizanur Khondoker | R package for combining multiple scans |
| MVCClass | Elizabeth Whalen | Model-View-Controller (MVC) Classes |
| nem | Florian Markowetz | Nested Effects Models to reconstruct phenotypic hierarchies |
| nnNorm | Adi Laurentiu Tarca | Spatial and intensity based normalization of cDNA microarray data based on robust neural nets |
| oligo | Benilton Carvalho | Oligonucleotide Arrays |
| oligoClasses | Benilton Carvalho | Classes for high-throughput SNP arrays |
| 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. |
| ontoTools | Vince Carey | graphs and sparse matrices for working with ontologies; formal objects for nomenclatures with provenance management |
| 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 |
| pkgDepTools | Seth Falcon | Package Dependency Tools |
| 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 |
| puma | Richard Pearson | Propagating Uncertainty in Microarray Analysis |
| quantsmooth | Jan Oosting | Quantile smoothing and genomic visualization of array data |
| rama | Raphael Gottardo | Robust Analysis of MicroArrays |
| RBGL | Li Long | An interface to the BOOST graph library |
| Rdbi | Jianhua Zhang | Generic database methods |
| RdbiPgSQL | Jianhua Zhang | PostgreSQL access |
| reb | Karl J. Dykema | Regional Expression Biases |
| RefPlus | Kai-Ming Chang | A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods. |
| rflowcyt | N. LeMeur | Statistical tools and data structures for analytic flow cytometry |
| Rgraphviz | Li Long | Provides plotting capabilities for R graph objects |
| rHVDM | Martino Barenco | Hidden Variable Dynamic Modeling |
| Ringo | J. Toedling | R Investigation of ChIP-chip Oligoarrays |
| Rintact | Tony Chiang | Interface to EBI Intact protein interaction data base |
| RNAither | Nora Rieber | Statistical analysis of high-throughput RNAi screens |
| RpsiXML | Jitao David Zhang | R interface to PSI-MI 2.5 files |
| Rredland | VJ Carey | interface to redland RDF utilities |
| rsbml | Michael Lawrence | R support for SBML, using libsbml |
| 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 | Base classes and methods for high-throughput short-read sequencing data. |
| SIM | Maarten van Iterson | Integrated Analysis of gene expression and copynumber data |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |
| simulatorAPMS | Tony Chiang | Computationally simulates the AP-MS technology. |
| SLGI | Nolwenn Le Meur | Synthetic Lethal Genetic Interaction |
| snapCGH | Thomas Hardcastle | Segmentation, normalisation and processing of aCGH data. |
| SNPchip | Robert Scharpf | Classes and Methods for high throughput SNP chip data |
| spikeLI | Enrico Carlon | Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool |
| splicegear | Laurent Gautier | splicegear |
| spotSegmentation | Chris Fraley | Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots |
| stepNorm | Yuanyuan Xiao | Stepwise normalization functions for cDNA microarrays |
| tilingArray | W. Huber | Analysis of 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 | Methods for fitting Hidden Markov Models to SNP chip data |
| vsn | Wolfgang Huber | Variance stabilization and calibration for microarray data |
| weaver | Seth Falcon | Tools and extensions for processing Sweave documents |
| webbioc | Colin A. Smith | Bioconductor Web Interface |
| widgetInvoke | Jeff Gentry | Evaluation widgets for functions |
| widgetTools | Jianhua Zhang | Creates an interactive tcltk widget |
| xmapbridge | Tim Yates | Export plotting files to the xmapBridge for visualisation in X:Map |
| xps | Christian Stratowa | Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays |
| yaqcaffy | Laurent Gatto | Affymetrix expression data quality control and reproducibility analysis |