| 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. |
| 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 |
| altcdfenvs | Laurent Gautier | alternative cdfenvs |
| applera | Francesca Cordero | applera |
| arrayMagic | Andreas Buness | two-colour cDNA array quality control and preprocessing |
| beadarray | Mark Dunning | Quality control and low-level analysis of BeadArrays |
| cellHTS | Wolfgang Huber | Analysis of cell-based screens |
| codelink | Diego Díez | Manipulation of Codelink Bioarrays data. |
| gcrma | Z. Wu | Background Adjustment Using Sequence Information |
| genArise | IFC Development Team | Microarray Analysis tool |
| 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 |
| maCorrPlot | Alexander Ploner | Visualize artificial correlation in microarray data |
| makecdfenv | James W. MacDonald | CDF Environment Maker |
| MANOR | Pierre Neuvial | Micro-Array NORmalization |
| marray | Yee Hwa (Jean) Yang | Exploratory analysis for two-color spotted microarray data |
| mmgmos | Xuejun Liu | multi-chip modified gamma Model of Oligonucleotide Signal |
| nnNorm | Laurentiu A. Tarca | Spatial and intensity based normalization of cDNA microarray data based on robust neural nets |
| OLIN | Matthias Futschik | Optimized local intensity-dependent normalisation of two-color microarrays |
| OLINgui | Matthias Futschik | Graphical user interface for OLIN |
| plier | Crispin Miller | Implements the Affymetrix PLIER algorithm |
| rama | Raphael Gottardo | Robust Analysis of MicroArrays |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |
| snapCGH | Mike Smith | Segmentation, normalisation and processing of aCGH data. |
| spotSegmentation | Chris Fraley | Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots |
| stepNorm | Yuanyuan Xiao | Stepwise normalization functions for cDNA microarrays |
| tilingArray | W. Huber | Analysis of high-density oligonucleotide tiling arrays |
| vsn | Wolfgang Huber | Variance stabilization and calibration for microarray data |