minfi - Analyze Illumina Infinium DNA methylation arrays

Tools to analyze & visualize Illumina Infinium methylation arrays.

Last updated 3 days ago

immunooncologydnamethylationdifferentialmethylationepigeneticsmicroarraymethylationarraymultichanneltwochanneldataimportnormalizationpreprocessingqualitycontrol

13.12 score 60 stars 34 packages 1.1k scripts 4.4k downloads

bsseq - Analyze, manage and store whole-genome methylation data

A collection of tools for analyzing and visualizing whole-genome methylation data from sequencing. This includes whole-genome bisulfite sequencing and Oxford nanopore data.

Last updated 24 days ago

dnamethylation

11.34 score 35 stars 16 packages 664 scripts 2.4k downloads

Rgraphviz - Provides plotting capabilities for R graph objects

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

Last updated 24 days ago

graphandnetworkvisualization

11.25 score 114 packages 1.3k scripts 14k downloads

illuminaio - Parsing Illumina Microarray Output Files

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

Last updated 24 days ago

infrastructuredataimportmicroarrayproprietaryplatformsbioconductor

10.39 score 6 stars 44 packages 50 scripts 4.5k downloads

affxparser - Affymetrix File Parsing SDK

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.

Last updated 24 days ago

infrastructuredataimportmicroarrayproprietaryplatformsonechannelbioconductor

7.82 score 7 stars 15 packages 65 scripts 2.3k downloads

cqn - Conditional quantile normalization

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

Last updated 24 days ago

immunooncologyrnaseqpreprocessingdifferentialexpression

5.94 score 4 packages 240 scripts 508 downloads