| Package | Maintainer | Title |
|---|---|---|
| ABarray | Yongming Andrew Sun | Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Micorarray (AB1700) gene expression data. |
| 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 |
| affylmGUI | Keith Satterley | GUI for affy analysis using limma package |
| 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) |
| annaffy | Colin A. Smith | Annotation tools for Affymetrix biological metadata |
| 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 |
| 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 |
| bridge | Raphael Gottardo | Bayesian Robust Inference for Differential Gene Expression |
| codelink | Diego Diez | Manipulation of Codelink Bioarrays data. |
| copa | James W. MacDonald | Functions to perform cancer outlier profile analysis. |
| exonmap | Crispin Miller | High level analysis of Affymetrix exon array data |
| gcrma | Z. Wu | Background Adjustment Using Sequence Information |
| GEOquery | Sean Davis | Get data from NCBI Gene Expression Omnibus (GEO) |
| 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 |
| lapmix | Yann Ruffieux | Laplace Mixture Model in Microarray Experiments |
| limma | Gordon Smyth | Linear Models for Microarray Data |
| lumi | Pan Du | BeadArray Specific Methods for Illumina Microarrays |
| maDB | Johannes Rainer | Microarray database and utility functions for microarray data analysis. |
| makecdfenv | James W. MacDonald | CDF Environment Maker |
| makePlatformDesign | Benilton Carvalho | Platform Design Package |
| oligo | Benilton Carvalho | Oligonucleotide Arrays |
| 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. |
| plw | Magnus Astrand | Probe level Locally moderated Weighted t-tests. |
| puma | Richard Pearson | Propagating Uncertainty in Microarray Analysis |
| RefPlus | Kai-Ming Chang | A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods. |
| RLMM | Nusrat Rabbee | A Genotype Calling Algorithm for Affymetrix SNP Arrays |
| SAGx | Per Broberg, | Statistical Analysis of the GeneChip |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |
| tilingArray | W. Huber | Analysis of high-density oligonucleotide tiling arrays |
| vsn | Wolfgang Huber | Variance stabilization and calibration for microarray data |
| webbioc | Colin A. Smith | Bioconductor Web Interface |
| 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 |