| Package | Maintainer | Title |
|---|---|---|
| ABarray | Yongming Andrew Sun | Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Micorarray (AB1700) gene expression data. |
| adSplit | Claudio Lottaz | Annotation-Driven Clustering |
| 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 |
| 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 |
| annotationTools | Alexandre Kuhn | Annotate microarrays and perform cross-species gene expression analyses using flat file databases. |
| 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 |
| 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 |
| BGmix | Alex Lewin | Bayesian models for differential gene expression |
| bgx | Ernest Turro | Bayesian Gene eXpression |
| BicARE | Pierre Gestraud | Biclustering Analysis and Results Exploration |
| bridge | Raphael Gottardo | Bayesian Robust Inference for Differential Gene Expression |
| CALIB | Hui Zhao | Calibration model for estimating absolute expression levels from microarray data |
| 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. |
| clippda | Stephen Nyangoma | A package for the clinical proteomic profiling data analysis |
| CNTools | J. Zhang | Convert segment data into a region by sample matrix to allow for other high level computational analyses. |
| 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. |
| 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 |
| DEDS | Yuanyuan Xiao | Differential Expression via Distance Summary for Microarray Data |
| DFP | Rodrigo Alvarez-Glez | Gene Selection |
| diffGeneAnalysis | Choudary Jagarlamudi | Performs differential gene expression Analysis |
| DNAcopy | Venkatraman E. Seshan | DNA copy number data analysis |
| 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 |
| exonmap | Crispin Miller | High level analysis of Affymetrix exon array data |
| explorase | Michael Lawrence | GUI for exploratory data analysis of systems biology data |
| factDesign | Denise Scholtens | Factorial designed microarray experiment analysis |
| fdrame | Effi Kenigsberg | FDR adjustments of Microarray Experiments (FDR-AME) |
| 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 |
| genefilter | Biocore Team c/o BioC user list | genefilter: methods for filtering genes from microarray experiments |
| geneRecommender | Greg Hather | A gene recommender algorithm to identify genes coexpressed with a query set of genes |
| GeneRegionScan | Lasse Folkersen | GeneRegionScan |
| GeneTraffic | Daniel Iordan | GeneTraffic R Integration Functions |
| GenomeGraphs | Steffen Durinck | Plotting genomic information from Ensembl |
| GEOquery | Sean Davis | Get data from NCBI Gene Expression Omnibus (GEO) |
| 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 |
| goTools | Agnes Paquet | Functions for Gene Ontology database |
| gpls | Biocore Team c/o BioC user list | Classification using generalized partial least squares |
| GSEAlm | Assaf Oron | Linear Model Toolset for Gene Set Enrichment Analysis |
| 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 |
| impute | Balasubramanian Narasimhan | impute: Imputation for microarray data |
| 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 |
| 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 | John Tillinghast | LMGene Software for Date Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays |
| 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. |
| 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 |
| maSigPro | Ana Conesa | Significant Gene Expression Profile Differences in Time Course Microarray Data |
| 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 |
| 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 |
| minet | Patrick E. Meyer | Mutual Information Network Inference |
| MiPP | Sukwoo Kim | Misclassification Penalized Posterior Classification |
| multiscan | Mizanur Khondoker | R package for combining multiple scans |
| multtest | Katherine S. Pollard | Resampling-based multiple hypothesis testing |
| 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 |
| 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. |
| 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. |
| 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 |
| pcot2 | Sarah Song | Principal Coordinates and Hotelling's T-Square method |
| PGSEA | Karl Dykema | Parametric Gene Set Enrichment Analysis |
| pickgene | Brian S. Yandell | Adaptive Gene Picking for Microarray Expression Data Analysis |
| plgem | Norman Pavelka | Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM) |
| 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. |
| puma | Richard Pearson | Propagating Uncertainty in Microarray Analysis |
| qpgraph | Robert Castelo | Reverse engineering of molecular regulatory networks with qp-graphs |
| rama | Raphael Gottardo | Robust Analysis of MicroArrays |
| rbsurv | Soo-heang Eo | Robust likelihood-based survival modeling with microarray data |
| 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. |
| 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 |
| RPA | Leo Lahti | RPA: probe reliability and differential gene expression analysis |
| RTools4TB | Aurelie Bergon | Data mining of public microarray data through connections to the TranscriptomeBrowser database. |
| SAGx | Per Broberg, | Statistical Analysis of the GeneChip |
| siggenes | Holger Schwender | Multiple testing using SAM and Efron's empirical Bayes approaches |
| SIM | Maarten van Iterson | Integrated Analysis on two human genomic datasets |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |
| sizepower | Weiliang Qiu | Sample Size and Power Calculation in Micorarray Studies |
| 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. |
| 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 |
| spotSegmentation | Chris Fraley | Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots |
| 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 |
| tilingArray | Zhenyu Xu | Transcript mapping with high-density oligonucleotide tiling arrays |
| timecourse | Yu Chuan Tai | Statistical Analysis for Developmental Microarray Time Course Data |
| 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 |
| vsn | Wolfgang Huber | Variance stabilization and calibration for microarray data |
| webbioc | Colin A. Smith | Bioconductor Web Interface |
| XDE | Robert Scharpf | XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression |
| 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 |