| Package | Maintainer | Title |
|---|---|---|
| AffyExpress | Xuejun Arthur Li | Affymetrix Quality Assessment and Analysis Tool |
| affylmGUI | Keith Satterley | GUI for affy analysis using limma package |
| affyPLM | Ben Bolstad | Methods for fitting probe-level models |
| affyQCReport | Craig Parman | QC Report Generation for affyBatch objects |
| altcdfenvs | Laurent Gautier | alternative CDF environments (aka probeset mappings) |
| 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 |
| beadarray | Mark Dunning | Quality assessment and low-level analysis for Illumina BeadArray data |
| dyebias | Philip Lijnzaad | The GASSCO method, for correcting for slide-depedent gene-specific dye bias |
| HELP | Reid F. Thompson | Tools for HELP data analysis |
| HTqPCR | Heidi Dvinge , Paul Bertone | Automated analysis of qPCR data |
| limma | Gordon Smyth | Linear Models for Microarray Data |
| limmaGUI | Keith Satterley | GUI for limma package |
| MANOR | Pierre Neuvial | CGH Micro-Array NORmalization |
| methylumi | Sean Davis | Handle Illumina methylation data |
| 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. |
| rama | Raphael Gottardo | Robust Analysis of MicroArrays |
| Ringo | J. Toedling | R Investigation of ChIP-chip Oligoarrays |
| RNAither | Nora Rieber | Statistical analysis of high-throughput RNAi screens |
| Rolexa | Jacques Rougemont | Statistical analysis of Solexa sequencing data |
| RPA | Leo Lahti | RPA: probe reliability and differential gene expression analysis |
| ShortRead | Biocore Team c/o BioC user list | Base classes and methods for high-throughput short-read sequencing data. |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |
| spikeLI | Enrico Carlon | Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool |
| spotSegmentation | Chris Fraley | Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots |
| Starr | Benedikt Zacher | Simple tiling array analysis of Affymetrix ChIP-chip data |
| yaqcaffy | Laurent Gatto | Affymetrix expression data quality control and reproducibility analysis |