Package: methrix 1.26.0

Anand Mayakonda

methrix: Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

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.

Authors:Anand Mayakonda [aut, cre], Reka Toth [aut], Rajbir Batra [ctb], Clarissa Feuerstein-Akgöz [ctb], Joschka Hey [ctb], Maximilian Schönung [ctb], Pavlo Lutsik [ctb]

methrix_1.26.0.tar.gz
methrix_1.26.0.zip(r-4.7)methrix_1.26.0.zip(r-4.6)methrix_1.26.0.zip(r-4.5)
methrix_1.26.0.tgz(r-4.6-any)methrix_1.26.0.tgz(r-4.5-any)
methrix_1.26.0.tar.gz(r-4.7-any)methrix_1.26.0.tar.gz(r-4.6-any)
methrix_1.26.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
methrix/json (API)
NEWS

# Install 'methrix' in R:
install.packages('methrix', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/compepigen/methrix/issues

Datasets:

On BioConductor:methrix-1.27.0(bioc 3.24)methrix-1.26.0(bioc 3.23)

dnamethylationsequencingcoveragebedgraphbioinformaticsdna-methylation

7.39 score 36 stars 57 scripts 446 downloads 27 exports 76 dependencies

Last updated from:fc39d16e2c (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING562
linux-devel-x86_64NOTE743
source / vignettesOK726
linux-release-x86_64NOTE690
macos-release-arm64NOTE512
macos-oldrel-arm64NOTE538
windows-develNOTE689
windows-releaseNOTE520
windows-oldrelNOTE1207
wasm-releaseOK392

Exports:combine_methrixconvert_HDF5_methrixconvert_methrixcoverage_filterextract_CPGsget_matrixget_region_summaryget_statsload_HDF5_methrixmask_methrixmethrix_pcamethrix_reportmethrix2bsseqorder_by_sdplot_coverageplot_densityplot_pcaplot_statsplot_violinread_bedgraphsregion_filterremove_snpsremove_uncoveredsave_HDF5_methrixsubset_methrixwrite_bedgraphswrite_bigwigs

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIObiocmakeBiocParallelBiostringsbitopsBSgenomecigarilloclicodetoolscpp11crayoncurldata.tableDelayedArrayDelayedMatrixStatsdir.expiryfarverfilelockformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtableh5mreadHDF5ArrayhttrIRangesisobandjsonlitelabelinglambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmimeopensslR6RColorBrewerRcppRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraysparseMatrixStatsSummarizedExperimentsysvctrsviridisLitewithrXMLXVectoryaml

Methrix tutorial

CompEpigen

Rendered frommethrix.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2020-10-23
Started: 2019-05-08