| Package | Maintainer | Title |
|---|---|---|
| ABarray | Yongming Andrew Sun | Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Micorarray (AB1700) gene expression data. |
| affy | Rafael A. Irizarry | Methods for Affymetrix Oligonucleotide Arrays |
| affycomp | Rafael A. Irizarry | Graphics Toolbox for Assessment of Affymetrix Expression Measures |
| AffyCompatible | Martin Morgan | Affymetrix GeneChip software compatibility |
| affycoretools | James W. MacDonald | Functions useful for those doing repetitive analyses with Affymetrix GeneChips. |
| AffyExpress | Xuejun Arthur Li | Affymetrix Quality Assessment and Analysis Tool |
| affyILM | Myriam Kroll and Fabrice Berger | Linear Model of background subtraction and the Langmuir isotherm |
| affylmGUI | Keith Satterley | GUI for affy analysis using limma package |
| affypdnn | Laurent Gautier | 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 |
| Agi4x44PreProcess | Pedro Lopez-Romero | PreProcessing of Agilent 4x44 array data |
| AgiMicroRna | Pedro Lopez-Romero | Processing and Differential Expression Analysis of Agilent microRNA chips |
| altcdfenvs | Laurent Gautier | alternative CDF environments (aka probeset mappings) |
| annaffy | Colin A. Smith | Annotation tools for Affymetrix biological metadata |
| aroma.light | Henrik Bengtsson | Light-weight methods for normalization and visualization of microarray data using only basic R data types |
| ArrayExpress | Audrey Kauffmann | Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet |
| 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 |
| bridge | Raphael Gottardo | Bayesian Robust Inference for Differential Gene Expression |
| clippda | Stephen Nyangoma | A package for the clinical proteomic profiling data analysis |
| codelink | Diego Diez | Manipulation of Codelink Bioarrays data. |
| copa | James W. MacDonald | Functions to perform cancer outlier profile analysis. |
| ExiMiR | Sylvain Gubian | R functions for the normalization of Exiqon miRNA array data |
| exonmap | Crispin Miller | High level analysis of Affymetrix exon array data (DEPRECATED please use xmapcore) |
| gage | Weijun Luo | Generally Applicable Gene-set Enrichment for Pathway Analysis |
| gcrma | Z. Wu | Background Adjustment Using Sequence Information |
| GeneRegionScan | Lasse Folkersen | GeneRegionScan |
| GEOquery | Sean Davis | Get data from NCBI Gene Expression Omnibus (GEO) |
| GlobalAncova | Manuela Hummel | Calculates a global test for differential gene expression between groups |
| globaltest | Jelle Goeman | Testing groups of covariates/features for association with a response variable, with applications to gene set testing |
| lapmix | Yann Ruffieux | Laplace Mixture Model in Microarray Experiments |
| limma | Gordon Smyth | Linear Models for Microarray Data |
| lumi | Pan Du | BeadArray Specific Methods for Illumina Methylation and Expression Microarrays |
| LVSmiRNA | Stefano Calza | LVS normalization for Agilent miRNA data |
| maDB | Johannes Rainer | Microarray database and utility functions for microarray data analysis. |
| makecdfenv | James W. MacDonald | CDF Environment Maker |
| makePlatformDesign | Benilton Carvalho | Platform Design Package |
| oligo | Benilton Carvalho | Preprocessing tools for oligonucleotide arrays. |
| 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. |
| plw | Magnus Astrand | Probe level Locally moderated Weighted t-tests. |
| PROMISE | Xueyuan Cao | PRojection Onto the Most Interesting Statistical Evidence |
| puma | Richard Pearson , Li Zhang | Propagating Uncertainty in Microarray Analysis |
| pvac | Jun Lu , Pierre R. Bushel | PCA-based gene filtering for Affymetrix arrays |
| RefPlus | Kai-Ming Chang | A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods. |
| RLMM | Nusrat Rabbee | A Genotype Calling Algorithm for Affymetrix SNP Arrays |
| RTools4TB | Aurelie Bergon | Data mining of public microarray data through connections to the TranscriptomeBrowser database. |
| SAGx | Per Broberg, | Statistical Analysis of the GeneChip |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |
| snm | Brig Mecham | Supervised Normalization of Microarrays |
| Starr | Benedikt Zacher | Simple tiling array analysis of Affymetrix ChIP-chip data |
| tilingArray | Zhenyu Xu | Transcript mapping with high-density oligonucleotide tiling arrays |
| TurboNorm | Maarten van Iterson | A fast scatterplot smoother suitable for microarray normalization |
| vsn | Wolfgang Huber | Variance stabilization and calibration for microarray data |
| webbioc | Colin A. Smith | Bioconductor Web Interface |
| xmapcore | Tim Yates | Core access to the xmap database (installed separately) |
| xps | Christian Stratowa | Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays |
| yaqcaffy | Laurent Gatto | Affymetrix expression data quality control and reproducibility analysis |