| 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. |
| 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 |
| affycoretools | James W. MacDonald | Functions useful for those doing repetitive analyses with Affymetrix GeneChips. |
| affydata | Laurent | Affymetrix Data for Demonstration Purpose |
| affyio | Benjamin Milo Bolstad | Tools for parsing Affymetrix data files |
| affylmGUI | Keith Satterley | GUI for affy analysis using limma package |
| affypdnn | Laurent | 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 |
| altcdfenvs | Laurent Gautier | alternative cdfenvs |
| annaffy | Colin A. Smith | Annotation tools for Affymetrix biological metadata |
| AnnBuilder | J. Zhang | Bioconductor annotation data package builder |
| annotate | Biocore Team | Annotation for microarrays |
| apComplex | Denise Scholtens | Estimate protein complex membership using AP-MS protein data |
| applera | Francesca Cordero | applera |
| aroma.light | Henrik Bengtsson | Light-weight methods for normalization and visualization of microarray data using only basic R data types |
| arrayMagic | Andreas Buness | two-colour cDNA array quality control and preprocessing |
| arrayQCplot | Eun-kyung Lee | Explore microarray data and check quality and reproducibility. |
| arrayQuality | A. Paquet | Assessing array quality on spotted arrays |
| beadarray | Mark Dunning | Quality control and low-level analysis of BeadArrays |
| beadarraySNP | Jan Oosting | Normalization and reporting of Illumina SNP bead arrays |
| BeadExplorer | Gareth Elvidge | QC, normalisation, annotation and exploration of Illumina BeadChip data |
| bim | Brian S. Yandell | Bayesian Interval Mapping Diagnostics |
| Biobase | Biocore Team | Biobase: Base functions for Bioconductor |
| biocViews | Seth Falcon | Categorized views of R package repositories |
| bioDist | Biocore Team | Different distance measures |
| biomaRt | Steffen Durinck | Interface to BioMart databases (e.g. Ensembl, Wormbase, Gramene and Uniprot) |
| BioMVCClass | Elizabeth Whalen | Model-View-Controller (MVC) Classes That Use Biobase |
| 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 |
| Category | S. Falcon | Category Analysis |
| cellHTS | Ligia Bras | Analysis of cell-based screens |
| cghMCR | J. Zhang | Find chromosome regions showing common gains/losses |
| ChromoViz | Jihoon Kim | Multimodal visualization of gene expression data |
| clusterStab | James W. MacDonald | Compute cluster stability scores for microarray 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. |
| ctc | Antoine Lucas | Cluster and Tree Conversion. |
| daMA | Jobst Landgrebe | Efficient design and analysis of factorial two-colour microarray data |
| DEDS | Yuanyuan Xiao | Differential Expression via Distance Summary for Microarray Data |
| diffGeneAnalysis | Choudary Jagarlamudi | Performs differential gene expression Analysis |
| DNAcopy | E. S. Venkatraman | DNA copy number data analysis |
| DynDoc | Biocore Team | Dynamic document tools |
| EBarrays | Deepayan Sarkar | Empirical Bayes for Microarrays |
| EBImage | Oleg Sklyar | Image processing and analysis toolkit for R |
| ecolitk | Laurent | Meta-data and tools for E. coli |
| edd | Vince Carey | expression density diagnostics |
| factDesign | Denise Scholtens | Factorial designed microarray experiment analysis |
| fdrame | Effi Kenigsberg | FDR adjustments of Microarray Experiments (FDR-AME) |
| gaggle | Paul Shannon | Broadcast data between R and Java bioinformatics programs |
| gcrma | Z. Wu | Background Adjustment Using Sequence Information |
| genArise | IFC Development Team | Microarray Analysis tool |
| genefilter | Biocore Team | genefilter: methods for filtering genes from microarray experiments |
| GeneMeta | Biocore Team | MetaAnalysis for High Throughput Experiments |
| geneplotter | Biocore Team | Grapics 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 |
| GeneSpring | Thon de Boer | GeneSpring R Integration Functions |
| GeneTraffic | Daniel Iordan | GeneTraffic R Integration Functions |
| GeneTS | Korbinian Strimmer | Microarray Time Series and Network Analysis |
| GEOquery | Sean Davis | Get data from NCBI Gene Expression Omnibus (GEO) |
| gff3Plotter | Oleg Sklyar | Plotting Data of Experiments on the Genomic Layout |
| GGtools | stvjc | software and data for genetical genomics (c) 2006 VJ Carey |
| GLAD | Philippe Hupé | Gain and Loss Analysis of DNA |
| GlobalAncova | R. Meister | Calculates a global test for differential gene expression between groups |
| globaltest | Jelle Goeman | Testing Association of Groups of Genes with a Clinical Variable |
| GOstats | S. Falcon | Tools for manipulating GO and microarrays. |
| goTools | Agnes Paquet | Functions for Gene Ontology database |
| gpls | Biocore Team | Classification using generalized partial least squares |
| graph | Seth Falcon | graph: A package to handle graph data structures |
| GraphAT | Thomas LaFramboise | Graph Theoretic Association Tests |
| Harshlight | Maurizio Pellegrino | A "corrective make-up" program for microarray chips |
| Heatplus | Alexander Ploner | A heat map displaying covariates and coloring clusters |
| HEM | HyungJun Cho | Heterogeneous error model for identification of differentially expressed genes under multiple conditions |
| hexbin | Nicholas Lewin-Koh | Hexagonal Binning Routines |
| hopach | Katherine S. Pollard | Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) |
| hypergraph | Seth Falcon | A package providing hypergraph data structures |
| Icens | Biocore Team | NPMLE for Censored and Truncated Data |
| idiogram | Karl J. Dykema | idiogram |
| impute | Balasubramanian Narasimhan | impute: Imputation for microarray data |
| iSNetwork | Elizabeth Whalen | Interactive Network Plots |
| iSPlot | Elizabeth Whalen | Linking Plots |
| KEGGSOAP | J. Zhang | Client-side SOAP access KEGG |
| lapmix | Yann Ruffieux | Laplace Mixture Model in Microarray Experiments |
| limma | Gordon Smyth | Linear Models for Microarray Data |
| limmaGUI | Keith Satterley | GUI for limma package |
| LMGene | Geun Cheol Lee | LMGene Software for Date Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays |
| logicFS | Holger Schwender | Identification of SNP Interactions |
| LPE | Nitin Jain | Methods for analyzing microarray data using Local Pooled Error (LPE) method |
| maanova | Lei Wu | 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 |
| makecdfenv | James W. MacDonald | CDF Environment Maker |
| 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 Differeneces in Time Course Microarray Data |
| matchprobes | Biocore Team | Tools for sequence matching of probes on arrays |
| MCRestimate | Markus Ruschhaupt | Misclassification error estimation with cross-validation |
| MeasurementError.cor | Beiying Ding | Measurement Error model estimate for correlation coefficient |
| MergeMaid | Xiaogang Zhong | Merge Maid |
| metaArray | Hyungwon Choi | Integration of Microarray Data for Meta-analysis |
| Mfuzz | Matthias Futschik | Soft clustering of time series gene expression data |
| MLInterfaces | V. Carey | Uniform interfaces to R machine learning procedures for data in Bioconductor containers |
| mmgmos | Xuejun Liu | multi-chip modified gamma Model of Oligonucleotide Signal |
| multtest | Katherine S. Pollard | Resampling-based multiple hypothesis testing |
| MVCClass | Elizabeth Whalen | Model-View-Controller (MVC) Classes |
| nem | Florian Markowetz | Nested Effects Models to reconstruct phenotypic hierarchies |
| nnNorm | Tarca Laurentiu | Spatial and intensity based normalization of cDNA microarray data based on robust neural nets |
| nudge | N. Dean | Normal Uniform Differential Gene Expression detection |
| OCplus | Alexander Ploner | Operating characteristics plus sample size and local fdr for microarray experiments |
| OLIN | Matthias Futschik | Optimized local intensity-dependent normalisation of two-color microarrays |
| OLINgui | Matthias Futschik | Graphical user interface for OLIN |
| 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 |
| pairseqsim | Witold Wolski | pairwise sequence alignment similarity simple. |
| pamr | Rob TIbshirani | Pam: prediction analysis for microarrays |
| panp | Peter Warren | Presence-Absence Calls from Negative Strand Matching Probesets |
| pathRender | Li Long | Render molecular pathways |
| pcaMethods | Wolfram Stacklies | A collection of PCA methods. |
| pcot2 | Sarah Song | Principle Coordinates and Hotelling's T-Square method |
| pdmclass | James W. MacDonald | Classification of Microarray Samples using Penalized Discriminant Methods |
| 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 |
| plgem | Mattia Pelizzola | Power Law Global Error Model |
| plier | Crispin Miller | Implements the Affymetrix PLIER algorithm |
| ppiStats | Tony Chiang | Protein-Protein Interaction Statistical Package |
| prada | Florian Hahne | Data analysis for cell-based functional assays |
| PROcess | Xiaochun Li | Ciphergen SELDI-TOF Processing |
| 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 | Interface to boost C++ graph lib |
| Rdbi | Jianhua Zhang | Generic database methods |
| RdbiPgSQL | Jianhua Zhang | PostgreSQL access |
| reb | Karl J. Dykema | Regional Expression Biases |
| Resourcerer | Jianhua Zhang | Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge. |
| rflowcyt | N. Le Meur | Statistical tools and data structures for analytic flow cytometry |
| Rgraphviz | Jeff Gentry | Provides plotting capabilities for R graph objects |
| RMAGEML | Steffen Durinck | Handling MAGEML documents |
| RMAPPER | VJ Carey | interface to mapper.chip.org |
| ROC | Vince Carey | utilities for ROC, with uarray focus |
| Rredland | VJ Carey | interface to redland RDF utilities |
| RSNPper | VJ Carey | interface to chip.org::SNPper for SNP-related data |
| Ruuid | Biocore Team | Ruuid: Provides Universally Unique ID values |
| safe | William T. Barry | Significance Analysis of Function and Expression |
| SAGElyzer | Jianhua Zhang | A package that deals with SAGE libraries |
| 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 |
| siggenes | Holger Schwender | SAM and Efron's empirical Bayes approaches |
| sigPathway | Weil Lai | Pathway Analysis |
| 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 |
| snapCGH | Mike Smith | Segmentation, normalisation and processing of aCGH data. |
| spikeLI | Enrico Carlon | Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool |
| splicegear | Laurent | splicegear |
| splots | Oleg Sklyar | Visualization routines for high throughput screens |
| 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 Microarry Sample Size |
| stam | Claudio Lottaz | Structured Analysis of Microarray Data |
| stepNorm | Yuanyuan Xiao | Stepwise normalization functions for cDNA microarrays |
| tilingArray | W. Huber | Analysis of high-density oligonucleotide tiling arrays |
| timecourse | Yu Chuan Tai | Statistical Analysis for Developmental Microarray Time Course Data |
| tkWidgets | J. Zhang | R based tk widgets |
| twilight | Stefanie Scheid | Estimation of local false discovery rate |
| TypeInfo | Duncan Temple Lang | Optional Type Specification Prototype |
| 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 |
| xcms | Colin A. Smith | LC/MS and GC/MS Data Analysis |