| 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 |
| clstutils | Noah Hoffman | Tools for performing taxonomic assignment. |
| dyebias | Philip Lijnzaad | The GASSCO method for correcting for slide-dependent gene-specific dye bias |
| farms | Djork-Arne Clevert | FARMS - Factor Analysis for Robust Microarray Summarization |
| flowPhyto | David M. Schruth | Methods for Continuous Flow Cytometry |
| Harshlight | Maurizio Pellegrino | A "corrective make-up" program for microarray chips |
| HELP | Reid F. Thompson | Tools for HELP data analysis |
| HTqPCR | Heidi Dvinge | Automated analysis of high-throughput qPCR data |
| ibh | Kircicegi Korkmaz | Interaction Based Homogeneity for Evaluating Gene Lists |
| limma | Gordon Smyth | Linear Models for Microarray Data |
| limmaGUI | Keith Satterley | GUI for limma package |
| lumi | Pan Du | BeadArray Specific Methods for Illumina Methylation and Expression Microarrays |
| MANOR | Pierre Neuvial | CGH Micro-Array NORmalization |
| mdqc | Gabriela Cohen-Freue | Mahalanobis Distance Quality Control for microarrays |
| MEDIPS | Lukas Chavez | MeDIP-Seq data analysis |
| 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. Next Generation Sequencing secondary analysis for ncRNA quantification is also available. |
| pvac | Jun Lu , Pierre R. Bushel | PCA-based gene filtering for Affymetrix arrays |
| R453Plus1Toolbox | Hans-Ulrich Klein | A package for importing and analyzing data from Roche's Genome Sequencer System. |
| rama | Raphael Gottardo | Robust Analysis of MicroArrays |
| RBioinf | Robert Gentleman | RBioinf |
| Ringo | J. Toedling | R Investigation of ChIP-chip Oligoarrays |
| RNAinteract | Bernd Fischer | Estimate Pairwise Interactions from multidimensional features |
| 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 | Classes and methods for high-throughput short-read sequencing data. |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |
| snm | Brig Mecham | Supervised Normalization of Microarrays |
| 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 |
| TEQC | Manuela Hummel | Quality control for target capture experiments |
| yaqcaffy | Laurent Gatto | Affymetrix expression data quality control and reproducibility analysis |