| Package | Maintainer | Title |
|---|---|---|
| aCGH | Peter Dimitrov | Classes and functions for Array Comparative Genomic Hybridization data. |
| affxparser | Kasper Daniel Hansen | Affymetrix File Parsing SDK |
| affyio | Benjamin Milo Bolstad | Tools for parsing Affymetrix data files |
| affylmGUI | Keith Satterley | GUI for affy analysis using limma package |
| ArrayExpress | Audrey Kauffmann | Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet |
| beadarraySNP | Jan Oosting | Normalization and reporting of Illumina SNP bead arrays |
| codelink | Diego Diez | Manipulation of Codelink Bioarrays data. |
| ctc | Antoine Lucas | Cluster and Tree Conversion. |
| exonmap | Crispin Miller | High level analysis of Affymetrix exon array data (DEPRECATED please use xmapcore) |
| GeneRegionScan | Lasse Folkersen | GeneRegionScan |
| genomeIntervals | Julien Gagneur | Operations on genomic intervals |
| GEOquery | Sean Davis | Get data from NCBI Gene Expression Omnibus (GEO) |
| 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 |
| makecdfenv | James W. MacDonald | CDF Environment Maker |
| MANOR | Pierre Neuvial | CGH Micro-Array NORmalization |
| MassArray | Reid F. Thompson | Analytical Tools for MassArray Data |
| 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. |
| Ringo | J. Toedling | R Investigation of ChIP-chip Oligoarrays |
| Rolexa | Jacques Rougemont | Statistical analysis of Solexa sequencing data |
| Rsamtools | Biocore Team c/o BioC user list | Import aligned BAM file format sequences into R / Bioconductor |
| RTools4TB | Aurelie Bergon | Data mining of public microarray data through connections to the TranscriptomeBrowser database. |
| rtracklayer | Michael Lawrence | R interface to genome browsers and their annotation tracks |
| SAGx | Per Broberg, | Statistical Analysis of the GeneChip |
| 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 |
| SRAdb | Jack Zhu | A compilation of metadata from NCBI SRA and tools |
| Starr | Benedikt Zacher | Simple tiling array analysis of Affymetrix ChIP-chip data |
| xps | Christian Stratowa | Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays |