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'))

Peer review:

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

7.04 score 31 stars 39 scripts 217 downloads 27 exports 84 dependencies

Last updated 3 months agofrom:7d44855bca. Checks:1 OK, 6 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKDec 29 2024
R-4.5-winNOTEDec 31 2024
R-4.5-linuxNOTEDec 29 2024
R-4.4-winNOTEDec 31 2024
R-4.4-macNOTEDec 29 2024
R-4.3-winNOTENov 29 2024
R-4.3-macNOTEDec 29 2024

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.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtableHDF5ArrayhttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigR6RColorBrewerRcppRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalessnowSparseArraysparseMatrixStatsSummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc

Methrix tutorial

CompEpigen

Rendered frommethrix.Rmdusingknitr::rmarkdownon Dec 29 2024.

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