| Package | Maintainer | Title |
|---|---|---|
| ABarray | Yongming Andrew Sun | Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Micorarray (AB1700) gene expression data. |
| aCGH | Peter Dimitrov | Classes and functions for Array Comparative Genomic Hybridization data. |
| ACME | Sean Davis | Algorithms for Calculating Microarray Enrichment (ACME) |
| adSplit | Claudio Lottaz | Annotation-Driven Clustering |
| 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 |
| AffyTiling | Charles G. Danko | Easy extraction of individual probes in Affymetrix tiling arrays |
| Agi4x44PreProcess | Pedro Lopez-Romero | PreProcessing of Agilent 4x44 array data |
| AgiMicroRna | Pedro Lopez-Romero | Processing and Differential Expression Analysis of Agilent microRNA chips |
| altcdfenvs | Laurent Gautier | alternative CDF environments (aka probeset mappings) |
| annaffy | Colin A. Smith | Annotation tools for Affymetrix biological metadata |
| annotate | Biocore Team c/o BioC user list | Annotation for microarrays |
| AnnotationDbi | Biocore Team c/o BioC user list | Annotation Database Interface |
| annotationTools | Alexandre Kuhn | Annotate microarrays and perform cross-species gene expression analyses using flat file databases. |
| 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 |
| BAC | Raphael Gottardo | Bayesian Analysis of Chip-chip experiment |
| baySeq | Thomas J. Hardcastle | Empirical Bayesian analysis of patterns of differential expression in count data |
| BCRANK | Adam Ameur | Predicting binding site consensus from ranked DNA sequences |
| beadarray | Mark Dunning | Quality assessment and low-level analysis for Illumina BeadArray data |
| beadarraySNP | Jan Oosting | Normalization and reporting of Illumina SNP bead arrays |
| betr | Martin Aryee | Identify differentially expressed genes in microarray time-course data |
| bgafun | Iain Wallace | BGAfun A method to identify specifity determining residues in protein families |
| BGmix | Alex Lewin | Bayesian models for differential gene expression |
| bgx | Ernest Turro | Bayesian Gene eXpression |
| BicARE | Pierre Gestraud | Biclustering Analysis and Results Exploration |
| 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 |
| bioDist | Biocore Team c/o BioC user list | Different distance measures |
| biomaRt | Steffen Durinck | Interface to BioMart databases (e.g. Ensembl, Wormbase and Gramene) |
| BioMVCClass | Elizabeth Whalen | Model-View-Controller (MVC) Classes That Use Biobase |
| BioSeqClass | Li Hong | Classification for Biological Sequences |
| Biostrings | H. Pages | String objects representing biological sequences, and matching algorithms |
| bridge | Raphael Gottardo | Bayesian Robust Inference for Differential Gene Expression |
| 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 |
| BUS | Yin Jin | Gene network reconstruction |
| CALIB | Hui Zhao | Calibration model for estimating absolute expression levels from microarray data |
| CAMERA | Carsten Kuhl | Collection of annotation related methods for mass spectrometry data |
| Category | Robert Gentleman | Category Analysis |
| 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. |
| cghMCR | J. Zhang | Find chromosome regions showing common gains/losses |
| CGHnormaliter | Bart P.P. van Houte | Normalization of array CGH data with imbalanced aberrations. |
| CGHregions | Mark van de Wiel | Dimension Reduction for Array CGH Data with Minimal Information Loss. |
| ChemmineR | Y. Eddie Cao | A Compound Data Mining Framework |
| ChIPpeakAnno | Lihua Julie Zhu | Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. |
| chipseq | Biocore Team c/o BioC user list | chipseq: A package for analyzing chipseq 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 |
| clippda | Stephen Nyangoma | A package for the clinical proteomic profiling data analysis |
| clusterStab | James W. MacDonald | Compute cluster stability scores for microarray data |
| CMA | Christoph Bernau | Synthesis of microarray-based classification |
| CNTools | J. Zhang | Convert segment data into a region by sample matrix to allow for other high level computational analyses. |
| CNVtools | Chris Barnes | A package to test genetic association with CNV data |
| CoCiteStats | R. Gentleman | Different test statistics based on co-citation. |
| 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. |
| cosmo | Oliver Bembom | Supervised detection of conserved motifs in DNA sequences |
| cosmoGUI | Oliver Bembom | GUI for constructing constraint sets used by the cosmo package |
| crlmm | Benilton S Carvalho , Robert Scharpf , Matt Ritchie | Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays. |
| ctc | Antoine Lucas | Cluster and Tree Conversion. |
| cycle | Matthias Futschik | Significance of periodic expression pattern in time-series data |
| daMA | Jobst Landgrebe | Efficient design and analysis of factorial two-colour microarray data |
| ddCt | Jitao David Zhang | The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR) |
| DEDS | Yuanyuan Xiao | Differential Expression via Distance Summary for Microarray Data |
| DEGseq | Likun Wang | Identify Differentially Expressed Genes from RNA-seq data |
| DFP | Rodrigo Alvarez-Glez | Gene Selection |
| diffGeneAnalysis | Choudary Jagarlamudi | Performs differential gene expression Analysis |
| DNAcopy | Venkatraman E. Seshan | DNA copy number data analysis |
| domainsignatures | Florian Hahne | Geneset enrichment based on InterPro domain signatures |
| dualKS | Eric J. Kort | Dual KS Discriminant Analysis and Classification |
| dyebias | Philip Lijnzaad | The GASSCO method, for correcting for slide-depedent gene-specific dye bias |
| DynDoc | Biocore Team c/o BioC user list | Dynamic document tools |
| EBarrays | Ming Yuan | Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification |
| EBImage | Gregoire Pau | Image processing toolbox for R |
| ecolitk | Laurent | Meta-data and tools for E. coli |
| edd | Vince Carey | expression density diagnostics |
| edgeR | Mark Robinson , Davis McCarthy , Gordon Smyth | Empirical analysis of digital gene expression data in R |
| 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 |
| factDesign | Denise Scholtens | Factorial designed microarray experiment analysis |
| fbat | The R Genetics Project | Family Based Association Tests for genetic data. |
| fdrame | Effi Kenigsberg | FDR adjustments of Microarray Experiments (FDR-AME) |
| flagme | Mark Robinson | Analysis of Metabolomics GC/MS Data |
| flowClust | Raphael Gottardo | Clustering for Flow Cytometry |
| flowCore | F. Hahne | flowCore: Basic structures for flow cytometry data |
| flowFlowJo | John J. Gosink | Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm. |
| flowFP | Herb Holyst | Fingerprinting for Flow Cytometry |
| flowMerge | Greg Finak | Cluster Merging for Flow Cytometry Data |
| flowQ | F. Hahne | Qualitiy control for flow cytometry |
| flowStats | Florian Hahne and Chao-Jen Wong | Statistical methods for the analysis of flow cytometry data |
| flowUtils | Nishant Gopalakrishnan | Utilities for flow cytometry |
| flowViz | Florian Hahne | Visualization for flow cytometry |
| gaga | David Rossell | GaGa hierarchical model for microarray data analysis |
| 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 |
| 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 |
| genefilter | Biocore Team c/o BioC user list | genefilter: methods for filtering genes from microarray experiments |
| GeneMeta | Biocore Team c/o BioC user list | MetaAnalysis for High Throughput Experiments |
| geneplotter | Biocore Team c/o BioC user list | Graphics related functions for Bioconductor |
| GeneR | Y. d'Aubenton-Carafa | R for genes and sequences analysis |
| geneRecommender | Greg Hather | A gene recommender algorithm to identify genes coexpressed with a query set of genes |
| GeneRegionScan | Lasse Folkersen | GeneRegionScan |
| GeneRfold | Antoine Lucas | R for genes and sequences, using viennaRNA package (fold) |
| GeneSelectMMD | Weiliang Qiu | Gene selection based on the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributions |
| GeneSelector | Martin Slawski | Stability and Aggregation of ranked gene lists |
| GeneSpring | Thon de Boer | GeneSpring R Integration Functions |
| GeneticsBase | The R Genetics Project | Classes and functions for handling genetic data |
| GeneticsDesign | The R Genetics Project | Functions for designing genetics studies |
| GeneticsPed | The R Genetics Project | Pedigree and genetic relationship 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 | Support package for genomic annotations |
| Genominator | James Bullard | Analyze genomic data |
| GEOmetadb | Jack Zhu | A compilation of metadata from NCBI GEO |
| GEOquery | Sean Davis | Get data from NCBI Gene Expression Omnibus (GEO) |
| GGBase | Vince Carey | infrastructure for genetics of gene expression (c) 2008 VJ Carey |
| GGtools | Vince Carey | software and data for genetical genomics (c) 2006 VJ Carey |
| GLAD | Philippe Hupe | Gain and Loss Analysis of DNA |
| GlobalAncova | R. Meister | Calculates a global test for differential gene expression between groups |
| globaltest | Jelle Goeman | Testing groups of covariates/features for association with a response variable, with applications to gene set testing |
| goProfiles | Alex Sanchez | goProfiles: an R package for the statistical analysis of functional profiles |
| GOSemSim | Guangchuang Yu | GO-terms Semantic Similarity Measures |
| GOstats | Robert Gentleman | Tools for manipulating GO and microarrays. |
| goTools | Agnes Paquet | Functions for Gene Ontology database |
| gpls | Biocore Team c/o BioC user list | Classification using generalized partial least squares |
| 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 |
| GSEAlm | Assaf Oron | Linear Model Toolset for Gene Set Enrichment Analysis |
| Harshlight | Maurizio Pellegrino | A "corrective make-up" program for microarray chips |
| Heatplus | Alexander Ploner | A heat map displaying covariates and coloring clusters |
| HELP | Reid F. Thompson | Tools for HELP data analysis |
| HEM | HyungJun Cho | Heterogeneous error model for identification of differentially expressed genes under multiple conditions |
| hexbin | Nicholas Lewin-Koh | Hexagonal Binning Routines |
| HilbertVis | Simon Anders | Hilbert curve visualization |
| HilbertVisGUI | Simon Anders | HilbertVisGUI |
| hopach | Katherine S. Pollard | Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) |
| HTqPCR | Heidi Dvinge , Paul Bertone | Automated analysis of qPCR data |
| 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 |
| impute | Balasubramanian Narasimhan | impute: Imputation for microarray data |
| IRanges | Biocore Team c/o BioC user list | Infrastructure for manipulating intervals on sequences |
| ITALICS | Guillem Rigaill | ITALICS |
| iterativeBMA | Ka Yee Yeung | The Iterative Bayesian Model Averaging (BMA) algorithm |
| iterativeBMAsurv | Ka Yee Yeung | The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis |
| 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 |
| keggorth | VJ Carey | graph support for KO, KEGG Orthology |
| KEGGSOAP | Robert Gentleman | Client-side SOAP access KEGG |
| lapmix | Yann Ruffieux | Laplace Mixture Model in Microarray Experiments |
| LBE | Cyril Dalmasso | Estimation of the false discovery rate. |
| limma | Gordon Smyth | Linear Models for Microarray Data |
| limmaGUI | Keith Satterley | GUI for limma package |
| LiquidAssociation | Yen-Yi Ho | LiquidAssociation |
| LMGene | John Tillinghast | LMGene Software for Date Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays |
| logicFS | Holger Schwender | Identification of SNP Interactions |
| logitT | Tobias Guennel | logit-t Package |
| LPE | Nitin Jain | Methods for analyzing microarray data using Local Pooled Error (LPE) method |
| 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. |
| lumi | Pan Du | BeadArray Specific Methods for Illumina Microarrays |
| maanova | Keith Sheppard | Tools for analyzing Micro Array experiments |
| 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. |
| made4 | Aedin Culhane | Multivariate analysis of microarray data using ADE4 |
| 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 |
| MantelCorr | Brian Steinmeyer | Compute Mantel Cluster Correlations |
| marray | Yee Hwa (Jean) Yang | Exploratory analysis for two-color spotted microarray data |
| maSigPro | Ana Conesa | Significant Gene Expression Profile Differences in Time Course Microarray Data |
| MassSpecWavelet | Pan Du | Mass spectrum processing by wavelet-based algorithms |
| matchprobes | Biocore Team c/o BioC user list | Basic infrastructure for using oligonucleotide microarray reporter sequence information for preprocessing and quality assessment |
| mBPCR | P.M.V. Rancoita | Bayesian Piecewise Constant Regression for DNA copy number estimation |
| MCRestimate | Marc Johannes | Misclassification error estimation with cross-validation |
| mdqc | Gabriela Cohen-Freue | Mahalanobis Distance Quality Control for microarrays |
| MeasurementError.cor | Beiying Ding | Measurement Error model estimate for correlation coefficient |
| MEDME | Mattia Pelizzola | Modelling Experimental Data from MeDIP Enrichment |
| MergeMaid | Xiaogang Zhong | Merge Maid |
| metaArray | Hyungwon Choi | Integration of Microarray Data for Meta-analysis |
| metahdep | John R. Stevens | Hierarchical Dependence in Meta-Analysis |
| methylumi | Sean Davis | Handle Illumina methylation data |
| Mfuzz | Matthias Futschik | Soft clustering of time series gene expression data |
| MiChip | Jonathon Blake | MiChip Parsing and Summarizing Functions |
| microRNA | Robert Gentleman | Data and functions for dealing with microRNAs |
| minet | Patrick E. Meyer | Mutual Information Network Inference |
| MiPP | Sukwoo Kim | Misclassification Penalized Posterior Classification |
| miRNApath | James M. Ward | miRNApath: Pathway Enrichment for miRNA Expression Data |
| MLInterfaces | V. Carey | Uniform interfaces to R machine learning procedures for data in Bioconductor containers |
| multiscan | Mizanur Khondoker | R package for combining multiple scans |
| multtest | Katherine S. Pollard | Resampling-based multiple hypothesis testing |
| MVCClass | Elizabeth Whalen | Model-View-Controller (MVC) Classes |
| nem | Christian Bender | 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 |
| nudge | N. Dean | Normal Uniform Differential Gene Expression detection |
| occugene | Oliver Will | Functions for Multinomial Occupancy Distribution |
| OCplus | Alexander Ploner | Operating characteristics plus sample size and local fdr for microarray experiments |
| oligo | Benilton Carvalho | Tools for low-level analysis of oligonucleotide arrays. |
| oligoClasses | Benilton Carvalho | Classes for high-throughput arrays supported by oligo |
| 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 |
| OrderedList | Claudio Lottaz | Similarities of Ordered Gene Lists |
| OutlierD | Sukwoo Kim | Outlier detection using quantile regression on the M-A scatterplots of high-throughput data |
| pamr | Rob Tibshirani | Pam: prediction analysis for microarrays |
| PAnnBuilder | Li Hong | Protein annotation data package builder |
| panp | Peter Warren | Presence-Absence Calls from Negative Strand Matching Probesets |
| parody | VJ Carey | Parametric And Resistant Outlier DYtection |
| pathRender | Li Long | Render molecular pathways |
| pcaMethods | Wolfram Stacklies | A collection of PCA methods. |
| pcot2 | Sarah Song | Principal Coordinates and Hotelling's T-Square method |
| PCpheno | Nolwenn Le Meur | Phenotypes and cellular organizational units |
| pdInfoBuilder | Benilton Carvalho | Platform Design Information Package Builder |
| pdmclass | James W. MacDonald | Classification of Microarray Samples using Penalized Discriminant Methods |
| PGSEA | Karl Dykema | Parametric Gene Set Enrichment Analysis |
| pgUtils | Johannes Rainer | Utility functions for PostgreSQL databases |
| pickgene | Brian S. Yandell | Adaptive Gene Picking for Microarray Expression Data Analysis |
| pkgDepTools | Seth Falcon | Package Dependency Tools |
| plateCore | Errol Strain | Statistical tools and data structures for plate-based flow cytometry |
| plgem | Norman Pavelka | Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM) |
| plier | Crispin Miller | Implements the Affymetrix PLIER algorithm |
| PLPE | Soo-heang Eo | Local Pooled Error Test for Differential Expression with Paired High-throughput Data |
| plw | Magnus Astrand | Probe level Locally moderated Weighted t-tests. |
| 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 |
| PROcess | Xiaochun Li | Ciphergen SELDI-TOF Processing |
| puma | Richard Pearson | Propagating Uncertainty in Microarray Analysis |
| qpcrNorm | Jessica Mar | Data-driven normalization strategies for high-throughput qPCR data. |
| qpgraph | Robert Castelo | Reverse engineering of molecular regulatory networks with qp-graphs |
| quantsmooth | Jan Oosting | Quantile smoothing and genomic visualization of array data |
| qvalue | John D. Storey | Q-value estimation for false discovery rate control |
| rama | Raphael Gottardo | Robust Analysis of MicroArrays |
| RankProd | Fangxin Hong | Rank Product method for identifying differentially expressed genes with application in meta-analysis |
| RbcBook1 | Vince Carey | Support for Springer monograph on Bioconductor |
| RBGL | Li Long | An interface to the BOOST graph library |
| RBioinf | Robert Gentleman | RBioinf |
| rbsurv | Soo-heang Eo | Robust likelihood-based survival modeling with microarray data |
| Rdbi | Jianhua Zhang | Generic database methods |
| RdbiPgSQL | Jianhua Zhang | PostgreSQL access |
| Rdisop | Steffen Neumann | Decomposition of Isotopic Patterns |
| reb | Karl J. Dykema | Regional Expression Biases |
| RefPlus | Kai-Ming Chang | A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods. |
| Resourcerer | Jianhua Zhang | Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge. |
| 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 |
| RLMM | Nusrat Rabbee | A Genotype Calling Algorithm for Affymetrix SNP Arrays |
| RMAGEML | Steffen Durinck | Handling MAGEML documents |
| Rmagpie | Camille Maumet | MicroArray Gene-expression-based Program In Error rate estimation |
| rMAT | Arnaud Droit and Raphael Gottardo | R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data. |
| RmiR | Francesco Favero | Package to work with miRNAs and miRNA targets with R |
| RNAither | Nora Rieber | Statistical analysis of high-throughput RNAi screens |
| ROC | Vince Carey | utilities for ROC, with uarray focus |
| Rolexa | Jacques Rougemont | Statistical analysis of Solexa sequencing data |
| RPA | Leo Lahti | RPA: probe reliability and differential gene expression analysis |
| 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 |
| 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 |
| Rtreemix | Jasmina Bogojeska | Rtreemix: Mutagenetic trees mixture models. |
| 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 |
| safe | William T. Barry | Significance Analysis of Function and Expression |
| sagenhaft | Tim Beissbarth | Collection of functions for reading and comparing SAGE libraries |
| SAGx | Per Broberg, | Statistical Analysis of the GeneChip |
| SBMLR | Tomas Radivoyevitch | SBML-R Interface and Analysis Tools |
| ScISI | Tony Chiang | In Silico Interactome |
| seqLogo | Oliver Bembom | Sequence logos for DNA sequence alignments |
| ShortRead | Biocore Team c/o BioC user list | Base classes and methods for high-throughput short-read sequencing data. |
| siggenes | Holger Schwender | Multiple testing using SAM and Efron's empirical Bayes approaches |
| sigPathway | Weil Lai | Pathway Analysis |
| 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. |
| sizepower | Weiliang Qiu | Sample Size and Power Calculation in Micorarray Studies |
| SJava | Martin Morgan | The Omegahat interface for R and Java. |
| SLGI | Nolwenn Le Meur | Synthetic Lethal Genetic Interaction |
| SLqPCR | Matthias Kohl | Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH |
| SMAP | Robin Andersson | A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling |
| snapCGH | John Marioni | Segmentation, normalisation and processing of aCGH data. |
| SNPchip | Robert Scharpf | Classes and Methods for high throughput SNP chip data |
| snpMatrix | David Clayton | The snp.matrix and X.snp.matrix classes |
| SpeCond | Florence Cavalli | Condition specific detection from expression data |
| SPIA | Adi Laurentiu Tarca | Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations |
| spikeLI | Enrico Carlon | Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool |
| spkTools | Matthew N McCall | Methods for Spike-in Arrays |
| splicegear | Laurent Gautier | splicegear |
| splots | Oleg Sklyar | Visualization of high-throughput assays in microtitre plate or chamber slide format |
| spotSegmentation | Chris Fraley | Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots |
| sscore | Richard Kennedy | S-Score Algorithm for Affymetrix Oligonucleotide Microarrays |
| ssize | Gregory R. Warnes | Estimate Microarray Sample Size |
| SSPA | Maarten van Iterson | Sample Size and Power Analysis for Microarray Data |
| Starr | Benedikt Zacher | Simple tiling array analysis of Affymetrix ChIP-chip data |
| stepNorm | Yuanyuan Xiao | Stepwise normalization functions for cDNA microarrays |
| TargetSearch | Alvaro Cuadros-Inostroza | A package for the analysis of GC-MS metabolite profiling data. |
| tilingArray | Zhenyu Xu | Transcript mapping with high-density oligonucleotide tiling arrays |
| timecourse | Yu Chuan Tai | Statistical Analysis for Developmental Microarray Time Course Data |
| tkWidgets | J. Zhang | R based tk widgets |
| topGO | Adrian Alexa | topGO: Enrichment analysis for Gene Ontology |
| tspair | Jeffrey T. Leek | Top Scoring Pairs for Microarray Classification |
| twilight | Stefanie Scheid | Estimation of local false discovery rate |
| TypeInfo | Duncan Temple Lang | Optional Type Specification Prototype |
| VanillaICE | Robert Scharpf | A Hidden Markov Model for high throughput genotyping arrays |
| vbmp | Nicola Lama | Variational Bayesian Multinomial Probit Regression |
| 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 |
| widgetTools | Jianhua Zhang | Creates an interactive tcltk widget |
| xcms | Colin A. Smith | LC/MS and GC/MS Data Analysis |
| XDE | Robert Scharpf | XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression |
| 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 |