Kasper Daniel Hansen

Kasper Daniel Hansen

8 packages on Bioconductor

affxparser

bioconductor
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Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.

bsseq

bioconductor
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A collection of tools for analyzing and visualizing bisulfite sequencing data.

cqn

bioconductor
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A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method.

illuminaio

bioconductor
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Tools for parsing Illumina's microarray output files, including IDAT.

minfi

bioconductor
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Tools for analyzing and visualizing Illumina's methylation array data.

Rgraphviz

bioconductor
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Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package.

bumphunter

bioconductor
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Tools for finding bumps in genomic data

shinyMethyl

bioconductor
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Interactive tool for visualizing Illumina's 450k array data