| 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 |
| 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 |
| bridge | Raphael Gottardo | Bayesian Robust Inference for Differential Gene Expression |
| 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 |
| 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 |
| EBarrays | Deepayan Sarkar | Empirical Bayes for Microarrays |
| 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 |
| genefilter | Biocore Team | 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 |
| GeneTraffic | Daniel Iordan | GeneTraffic R Integration Functions |
| GEOquery | Sean Davis | Get data from NCBI Gene Expression Omnibus (GEO) |
| gff3Plotter | Oleg Sklyar | Plotting Data of Experiments on the Genomic Layout |
| 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 |
| goTools | Agnes Paquet | Functions for Gene Ontology database |
| gpls | Biocore Team | Classification using generalized partial least squares |
| 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 |
| impute | Balasubramanian Narasimhan | impute: Imputation for microarray data |
| 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. |
| makecdfenv | James W. MacDonald | CDF Environment Maker |
| 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 Differeneces in Time Course Microarray Data |
| matchprobes | Biocore Team | Tools for sequence matching of probes on arrays |
| 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 |
| mmgmos | Xuejun Liu | multi-chip modified gamma Model of Oligonucleotide Signal |
| multtest | Katherine S. Pollard | Resampling-based multiple hypothesis testing |
| 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 |
| OrderedList | Claudio Lottaz | Similarities of Ordered Gene Lists |
| pamr | Rob TIbshirani | Pam: prediction analysis for microarrays |
| panp | Peter Warren | Presence-Absence Calls from Negative Strand Matching Probesets |
| pcot2 | Sarah Song | Principle Coordinates and Hotelling's T-Square method |
| pickgene | Brian S. Yandell | Adaptive Gene Picking for Microarray Expression Data Analysis |
| plgem | Mattia Pelizzola | Power Law Global Error Model |
| quantsmooth | Jan Oosting | Quantile smoothing and genomic visualization of array data |
| rama | Raphael Gottardo | Robust Analysis of MicroArrays |
| 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. |
| RMAGEML | Steffen Durinck | Handling MAGEML documents |
| RSNPper | VJ Carey | interface to chip.org::SNPper for SNP-related data |
| safe | William T. Barry | Significance Analysis of Function and Expression |
| SAGx | Per Broberg | Statistical Analysis of the GeneChip |
| siggenes | Holger Schwender | SAM and Efron's empirical Bayes approaches |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |
| sizepower | Weiliang Qiu | Sample Size and Power Calculation in Micorarray Studies |
| snapCGH | Mike Smith | Segmentation, normalisation and processing of aCGH data. |
| splicegear | Laurent | splicegear |
| spotSegmentation | Chris Fraley | Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots |
| 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 |
| 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 |