minfi - Analyze Illumina Infinium DNA methylation arrays

Tools to analyze & visualize Illumina Infinium methylation arrays.

Last updated 5 months ago

immunooncologydnamethylationdifferentialmethylationepigeneticsmicroarraymethylationarraymultichanneltwochanneldataimportnormalizationpreprocessingqualitycontrol

58 stars 12.96 score 134 dependencies 34 dependents

bsseq - Analyze, manage and store bisulfite sequencing data

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

Last updated 5 months ago

dnamethylation

35 stars 11.72 score 79 dependencies 16 dependents

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 12 days ago

graphandnetworkvisualization

11.24 score 2 dependencies 112 dependents

illuminaio - Parsing Illumina Microarray Output Files

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

Last updated 5 months ago

infrastructuredataimportmicroarrayproprietaryplatformsbioconductor

6 stars 10.38 score 4 dependencies 44 dependents

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 5 months ago

infrastructuredataimportmicroarrayproprietaryplatformsonechannelbioconductor

7 stars 8.81 score 0 dependencies 15 dependents

cqn - Conditional quantile normalization

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

Last updated 5 months ago

immunooncologyrnaseqpreprocessingdifferentialexpression

5.76 score 10 dependencies 4 dependents