| 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 |
| 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 |
| affyPara | Markus Schmidberger | Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays |
| affypdnn | Laurent Gautier | Probe Dependent Nearest Neighbours (PDNN) for the affy package |
| affyPLM | Ben Bolstad | Methods for fitting probe-level models |
| AffyTiling | Charles G. Danko | Easy extraction of individual probes in Affymetrix tiling arrays |
| 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) |
| aroma.light | Henrik Bengtsson | Light-weight methods for normalization and visualization of microarray data using only basic R data types |
| ArrayTools | Arthur Li | geneChip Analysis Package |
| beadarray | Mark Dunning | Quality assessment and low-level analysis for Illumina BeadArray data |
| beadarraySNP | Jan Oosting | Normalization and reporting of Illumina SNP bead arrays |
| BUS | Yuanhua Liu | Gene network reconstruction |
| CALIB | Hui Zhao | Calibration model for estimating absolute expression levels from microarray data |
| cellHTS2 | Florian Hahne | Analysis of cell-based screens - revised version of cellHTS |
| CGHcall | Mark van de Wiel | Calling aberrations for array CGH tumor profiles. |
| CGHnormaliter | Bart P.P. van Houte | Normalization of array CGH data with imbalanced aberrations. |
| codelink | Diego Diez | Manipulation of Codelink Bioarrays data. |
| crlmm | Benilton S Carvalho , Robert Scharpf , Matt Ritchie | Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays. |
| DEGseq | Likun Wang | Identify Differentially Expressed Genes from RNA-seq data |
| dyebias | Philip Lijnzaad | The GASSCO method, for correcting for slide-depedent gene-specific dye bias |
| exonmap | Crispin Miller | High level analysis of Affymetrix exon array data (DEPRECATED please use xmapcore) |
| frma | Matthew N. McCall | Frozen RMA and Barcode |
| frmaTools | Matthew N. McCall | Frozen RMA Tools |
| gcrma | Z. Wu | Background Adjustment Using Sequence Information |
| genArise | IFC Development Team | Microarray Analysis tool |
| HELP | Reid F. Thompson | Tools for HELP data analysis |
| HTqPCR | Heidi Dvinge | Automated analysis of high-throughput qPCR data |
| limma | Gordon Smyth | Linear Models for Microarray Data |
| limmaGUI | Keith Satterley | GUI for limma package |
| LMGene | Blythe Durbin-Johnson | LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays |
| lumi | Pan Du | BeadArray Specific Methods for Illumina Microarrays |
| maCorrPlot | Alexander Ploner | Visualize artificial correlation in microarray data |
| maigesPack | Gustavo H. Esteves | Functions to handle cDNA microarray data, including several methods of data analysis |
| makecdfenv | James W. MacDonald | CDF Environment Maker |
| makePlatformDesign | Benilton Carvalho | Platform Design Package |
| MANOR | Pierre Neuvial | CGH Micro-Array NORmalization |
| marray | Yee Hwa (Jean) Yang | Exploratory analysis for two-color spotted microarray data |
| methylumi | Sean Davis | Handle Illumina methylation data |
| Mfuzz | Matthias Futschik | Soft clustering of time series gene expression data |
| MiChip | Jonathon Blake | MiChip Parsing and Summarizing Functions |
| multiscan | Mizanur Khondoker | R package for combining multiple scans |
| nnNorm | Adi Laurentiu Tarca | Spatial and intensity based normalization of cDNA microarray data based on robust neural nets |
| oligo | Benilton Carvalho | Preprocessing tools for oligonucleotide arrays. |
| 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. |
| puma | Richard Pearson , Li Zhang | Propagating Uncertainty in Microarray Analysis |
| qpcrNorm | Jessica Mar | Data-driven normalization strategies for high-throughput qPCR data. |
| rama | Raphael Gottardo | Robust Analysis of MicroArrays |
| RefPlus | Kai-Ming Chang | A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods. |
| Ringo | J. Toedling | R Investigation of ChIP-chip Oligoarrays |
| rMAT | Arnaud Droit and Raphael Gottardo | R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data. |
| 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 |
| SAGx | Per Broberg, | Statistical Analysis of the GeneChip |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |
| snapCGH | John Marioni | Segmentation, normalisation and processing of aCGH data. |
| 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 |
| stepNorm | Yuanyuan Xiao | Stepwise normalization functions for cDNA microarrays |
| TargetSearch | Alvaro Cuadros-Inostroza | A package for the analysis of GC-MS metabolite profiling data. |
| tilingArray | Zhenyu Xu | Transcript mapping with high-density oligonucleotide tiling arrays |
| vsn | Wolfgang Huber | Variance stabilization and calibration for microarray data |
| xps | Christian Stratowa | Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays |