minfi - Analyze Illumina Infinium DNA methylation arrays
Tools to analyze & visualize Illumina Infinium methylation arrays.
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immunooncologydnamethylationdifferentialmethylationepigeneticsmicroarraymethylationarraymultichanneltwochanneldataimportnormalizationpreprocessingqualitycontrol
13.56 score 64 stars 35 dependents 2.3k scripts 7.4k downloadsbsseq - 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.
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dnamethylationcpp
13.15 score 38 stars 20 dependents 1.2k scripts 3.1k downloadsRgraphviz - 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.
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graphandnetworkvisualizationzlibglibc
11.29 score 116 dependents 1.7k scripts 17k downloadsilluminaio - Parsing Illumina Microarray Output Files
Tools for parsing Illumina's microarray output files, including IDAT.
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infrastructuredataimportmicroarrayproprietaryplatformsbioconductor
9.87 score 5 stars 40 dependents 1 scripts 8.9k downloadsaffxparser - 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.
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infrastructuredataimportmicroarrayproprietaryplatformsonechannelbioconductorcpp
8.81 score 8 stars 19 dependents 92 scripts 3.9k downloadscqn - Conditional quantile normalization
A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method.
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immunooncologyrnaseqpreprocessingdifferentialexpression
6.83 score 4 dependents 284 scripts 699 downloadsminfiData - Example data for the Illumina Methylation 450k array
Data from 6 samples across 2 groups from 450k methylation arrays.
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homo_sapiens_datamethylationarraydatamicroarraydatadatapkg
4.44 score 1 dependents 455 scriptsminfiDataEPIC - Example data for the Illumina Methylation EPIC array
Data from 3 technical replicates of the cell line GM12878 from the EPIC methylation array.
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homo_sapiens_datamethylationarraydatamicroarraydatadatapkg
2.72 score 26 scriptsbsseqData - Example whole genome bisulfite data for the bsseq package
Example whole genome bisulfite data for the bsseq package
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genomecancerdatacoloncancerdatasequencingdatadatapkg
2.56 score 18 scriptsIlluminaDataTestFiles - Illumina microarray files (IDAT) for testing
Example data for Illumina microarray output files, for testing purposes
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microarraydatadatapkg
2.38 score 12 scripts