| Package | Maintainer | Title |
|---|---|---|
| aCGH | Jane Fridlyand | Classes and functions for Array Comparative Genomic Hybridization data. |
| affxparser | Kasper Daniel Hansen | Affymetrix File Parsing SDK |
| affyio | Benjamin Milo Bolstad | Tools for parsing Affymetrix data files |
| affylmGUI | Keith Satterley | GUI for affy analysis using limma package |
| arrayMagic | Andreas Buness | two-colour cDNA array quality control and preprocessing |
| beadarraySNP | Jan Oosting | Normalization and reporting of Illumina SNP bead arrays |
| BeadExplorer | Gareth Elvidge | QC, normalisation, annotation and exploration of Illumina BeadChip data |
| codelink | Diego Diez | Manipulation of Codelink Bioarrays data. |
| ctc | Antoine Lucas | Cluster and Tree Conversion. |
| exonmap | Crispin Miller | High level analysis of Affymetrix exon array data |
| GEOquery | Sean Davis | Get data from NCBI Gene Expression Omnibus (GEO) |
| limma | Gordon Smyth | Linear Models for Microarray Data |
| limmaGUI | Keith Satterley | GUI for limma package |
| makecdfenv | James W. MacDonald | CDF Environment Maker |
| MANOR | Pierre Neuvial | CGH Micro-Array NORmalization |
| oneChannelGUI | Raffaele A Calogero | This package extends the capabilities of affylmGUI graphical interface. |
| Ringo | J. Toedling | R Investigation of NimbleGen Oligoarrays |
| SAGx | Per Broberg | Statistical Analysis of the GeneChip |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |