Package: methrix 1.21.0

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]

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methrix.pdf |methrix.html✨
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-1.21.0(bioc 3.21)methrix-1.20.0(bioc 3.20)

dnamethylationsequencingcoveragebedgraphbioinformaticsdna-methylation

7.53 score 32 stars 1 packages 39 scripts 310 downloads 27 exports 84 dependencies

Last updated 5 months agofrom:7d44855bca. Checks:1 OK, 8 NOTE. Indexed: yes.

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Doc / VignettesOKMar 29 2025
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R-4.3-winNOTEJan 28 2025
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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:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomeclicodetoolscolorspacecpp11crayoncurldata.tableDelayedArrayDelayedMatrixStatsfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtableh5mreadHDF5ArrayhttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigR6RColorBrewerRcppRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalessnowSparseArraysparseMatrixStatsSummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryaml

Methrix tutorial

CompEpigen

Rendered frommethrix.Rmdusingknitr::rmarkdownon Mar 29 2025.

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