epialleleR - Fast, Accurate, Epiallele-Aware Methylation Caller and Reporter
Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited. This package calls and reports cytosine methylation as well as frequencies of hypermethylated epialleles at the level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map (BAM) files as an input. Among other things, this package can also extract and visualise methylation patterns and assess allele specificity of methylation.
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dnamethylationepigeneticsmethylseqlongreadbioconductorcytosine-methylation-reportdna-methylationepialleleepimutationlong-read-sequencingnext-generation-sequencingsamtoolsshort-read-sequencingcurlbzip2xz-utilszlibcpp
5.86 score 6 stars 6 scripts 389 downloadsramr - Detection of Rare Aberrantly Methylated Regions in Array and NGS Data
ramr is an R package for detection of epimutations (i.e., infrequent aberrant DNA methylation events) in large data sets obtained by methylation profiling using array or high-throughput methylation sequencing. In addition, package provides functions to visualize found aberrantly methylated regions (AMRs), to generate sets of all possible regions to be used as reference sets for enrichment analysis, and to generate biologically relevant test data sets for performance evaluation of AMR/DMR search algorithms.
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dnamethylationdifferentialmethylationepigeneticsmethylationarraymethylseqaberrant-methylationbioconductordna-methylationepimutationmethylation-microarraysnext-generation-sequencingcppopenmp
4.65 score 5 scripts 392 downloads