Bioconductor

We contribute to the Bioconductor project.

affxparser: A package for parsing output files from Affymetrix microarrays using the Fusion SDK.
     [ download stats | build devel | build release | GitHub ]

bsseq: A package for analyzing whole-genome bisulfite sequencing data.
     [ download stats | build devel | build release | GitHub ]

bumphunter: A package implementing a general backend for the bumphunter approach.
     [ download stats | build devel | build release | GitHub ]

cqn: A package for normalizing RNA-seq data using the CQN algorithm.
     [ download stats | build devel | build release ]

Genominator: A package implementing a SQLite based backend for genomic data, including sequencing and microarrays.
     [ download stats | build devel | build release ]

illuminaio: A package for parsing output for Illumina microarrays.
     [ download stats | build devel | build release | GitHub ]

minfi: A package for analysing Illumina’s 450k methylation microarray.
     [ download stats | build devel | build release | GitHub ]

Rgraphviz: A package for visualizing graphs using the Graphviz toolkit.
     [ download stats | build devel | build release | GitHub ]

shinyMethyl: A package for interactive visualization and quality control of 450k arrays, using shiny.
     [ download stats | build devel | build release | GitHub ]

yamss: Software for MS-based metabolomics. Implements the bakedpi algorithm.
     [ download stats | build devel | build release | GitHub ]

Non Bioconductor

Myrna: Cloud-scale differential expression for RNA-seq.

Data packages (Bioconductor)

AffymetrixDataTestFiles: Affymetrix array files, for test purposes.
     [ build devel | build release ]

bsseqData: WGBS example data, for the bsseq package.
     [ build devel | build release ]

minfiData: 450k data example data, for the minfi package (and others).
     [ build devel | build release ]

IlluminaDataTestFiles: Illumina array files, for test purposes.
     [ build devel | build release ]

shinyMethylData: example summary data for the shinyMethyl package.
     [ build devel | build devel ]

Annotation packages (Bioconductor)

IlluminaHumanMethylation27kmanifest: annotation files for the 27k array.

IlluminaHumanMethylation450kmanifest: annotation files for the 450k array.

IlluminaHumanMethylation450kanno.ilmn12.hg19: annotation files for the 450k array.

IlluminaHumanMethylationEPICmanifest: annotation files for the EPIC array.

IlluminaHumanMethylationEPICanno.ilm10b2.hg19: annotation files for the EPIC array.