Package: methrix 1.27.0

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_1.27.0.tar.gz
methrix_1.27.0.zip(r-4.7)methrix_1.27.0.zip(r-4.6)methrix_1.27.0.zip(r-4.5)
methrix_1.27.0.tgz(r-4.6-any)methrix_1.27.0.tgz(r-4.5-any)
methrix_1.27.0.tar.gz(r-4.7-any)methrix_1.27.0.tar.gz(r-4.6-any)
methrix_1.27.0.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.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

7.41 score 36 stars 59 scripts 446 downloads 27 exports 77 dependencies

Last updated from:13c2ece168. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING483
linux-devel-x86_64NOTE754
source / vignettesOK706
linux-release-x86_64NOTE755
macos-release-arm64NOTE357
macos-oldrel-arm64NOTE458
windows-develNOTE613
windows-releaseNOTE566
windows-oldrelNOTE535
wasm-releaseOK425

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:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocParallelBiostringsbitopsBSgenomecigarilloclicodetoolscpp11crayoncurldata.tableDelayedArrayDelayedMatrixStatsdir.expiryfarverfilelockformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtableh5mreadHDF5ArrayhttrIRangesisobandjsonlitelabelinglambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmimeopensslR6RColorBrewerRcppRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraysparseMatrixStatsSummarizedExperimentsysvctrsviridisLitewithrXMLXVectoryaml

Methrix tutorial

CompEpigen

Rendered frommethrix.Rmdusingknitr::rmarkdownon May 30 2026.

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