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DNA Methylation

Parent category Analysis
Description Components that analyze DNA methylation data.
Component Version Inputs Outputs Description
BismarkAlign 1.0 reads, refGenome, mates methylationCalls, bedGraph, alignment, Mbias, report, analysis Performs alignment of bisulfite sequencing data in addition to deduplication and methylation extraction using Bismark Bisulfite Mapper.
BSAlign 1.0 reference, reads, mates alignedReads Aligns BS or RRBS data though BSMAP software, version 2.74.
DiffMeth 1.0 rawFilteredNormMethyl, regions plots, differentialMethylation, visualization, analysis Function to compute differential methylation at a base/window/region resolution.
DMML 1.0 input_files, sample_compositions, index_file params, probs, pvalues, map_estimates, expected_values, diff_meth Identifies differentially methylated sites in tumor samples with varying, unknown tumor cell fraction using a maximum-likelihood method.
ExprMethylCGH 1.1.1 exprMatrix, cghMatrix, methylMatrix statistics Integrates expression data with methylation and CGH data by using two label matrices of ones and zeros.
IlluminaAnnotator 13.10 in out Fetches genomic annotations for Illumina methylation and expression array probes.
MethFilterNorm 1.0 methCallArray, groupIDs rawFilteredNormMethyl, statistics, analysis, visualization Function loading the methylation calls data into a MethylRaw or MethylRawList object (MethylKit package data types) and performing normalization and filtering of the data.
MethylCall 1.0 reference, alignment methylationCalling Perform Methylation Calling of aligned RRBS and WGBS data obtained from the component BSalign.
WARNING: It requires quite a big amount of CPU (For human genome, needs ~26GB memory or more).
MethylExtract 1.0 bam, refGenome CpGmeth, CHGmeth, CHHmeth, SNVs, analysis Extracts methylation from a bam file simultaneously with variant calling.
SelectDiffMeth 1.0 differentialMethylation, features signifDiffMeth, plots, annotation, visualization Function to select which bases/windows/regions are significantly differentially methylated.
SelectMethContext 1.0 methCall cpg, chg, chh, statistics Separate cytosines based on the methylation context in which they occur and produces statistics about context methylation.

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