DOI: 10.18129/B9.bioc.methrix    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see methrix.

Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

Bioconductor version: 3.10

Bedgraph files generated by Bisulfite pipelines often come in various flavors. Critical downstream step requires summarization of these files into methylation/coverage matrices. This step of data aggregation is done by Methrix, including many other useful downstream functions.

Author: Anand Mayakonda [aut, cre], Reka Toth [aut], Maximilian Schönung [ctb], Pavlo Lutsik [ctb], Joschka Hey [ctb]

Maintainer: Anand Mayakonda <anand_mt at>

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biocViews Coverage, DNAMethylation, Sequencing, Software
Version 1.0.05
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
License MIT + file LICENSE
Depends R (>= 3.6), data.table (>= 1.12.4), SummarizedExperiment
Imports DelayedArray, HDF5Array, BSgenome, rjson, DelayedMatrixStats, parallel, methods, ggplot2, matrixStats, graphics, stats, utils
Suggests knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, GenomicScores, Biostrings, RColorBrewer, GenomicRanges, GenomeInfoDb, IRanges, testthat (>= 2.1.0)
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