| Package | Maintainer | Title |
|---|---|---|
| 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 |
| 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 |
| applera | Francesca Cordero | applera |
| beadarray | Mark Dunning | Quality control and low-level analysis of BeadArrays |
| bridge | Raphael Gottardo | Bayesian Robust Inference for Differential Gene Expression |
| codelink | Diego Díez | Manipulation of Codelink Bioarrays data. |
| copa | James W. MacDonald | Functions to perform cancer outlier profile analysis. |
| gcrma | Z. Wu | Background Adjustment Using Sequence Information |
| GEOquery | Sean Davis | Get data from NCBI Gene Expression Omnibus (GEO) |
| gff3Plotter | Oleg Sklyar | Plotting Data of Experiments on the Genomic Layout |
| 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 |
| limma | Gordon Smyth | Linear Models for Microarray Data |
| maDB | Johannes Rainer | Microarray database and utility functions for microarray data analysis. |
| makecdfenv | James W. MacDonald | CDF Environment Maker |
| mmgmos | Xuejun Liu | multi-chip modified gamma Model of Oligonucleotide Signal |
| panp | Peter Warren | Presence-Absence Calls from Negative Strand Matching Probesets |
| plier | Crispin Miller | Implements the Affymetrix PLIER algorithm |
| RLMM | Nusrat Rabbee | A Genotype Calling Algorithm for Affymetrix SNP Arrays |
| 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 |