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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 ]

bnbc: A package for normalization and removal of unwanted variation in Hi-C data.
[ 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 ]

mpra: A package for analysis of massively parallel reporter assays (MPRA).
[ 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.

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 ]

IlluminaHumanMethylation27kmanifest: annotation files for the 27k array.

IlluminaHumanMethylation450kmanifest: annotation files for the 450k array.

IlluminaHumanMethylationEPICmanifest: annotation files for the EPIC array.