Software (Bioconductor)
I am a contributor to the Bioconductor project.
affxparser: A package for
parsing output files from Affymetrix microarrays using the Fusion SDK.
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bsseq: A package for analyzing
whole-genome bisulfite sequencing data.
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bumphunter: A
package implementing a general backend for the bumphunter approach.
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cqn: A package for normalizing
RNA-seq data using the CQN algorithm.
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Genominator: A package
implementing a SQLite based backend for genomic data, including sequencing and microarrays.
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illuminaio: A package
for parsing output for Illumina microarrays.
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minfi: A package for analysing
Illumina's 450k methylation microarray.
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Rgraphviz: A package for
visualizing graphs using the Graphviz toolkit.
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Software (Non Bioconductor)
Myrna: Cloud-scale differential expression for RNA-seq.
shinyMethyl: Interactive visualization of 450k methylation data using Bioconductor and shiny.
Data packages (Bioconductor)
AffymetrixDataTestFiles:
Affymetrix array files, for test purposes.
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bsseqData: WGBS
example data, for the bsseq package.
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minfiData: 450k data
example data, for the minfi package (and others).
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IlluminaDataTestFiles:
Illumina array files, for test purposes.
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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.