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-1.19.0(bioc 3.20)methrix-1.18.0(bioc 3.19)

dnamethylationsequencingcoveragebedgraphbioinformaticsdna-methylation

6.98 score 28 stars 38 scripts 217 downloads 27 exports 83 dependencies

Last updated 22 days agofrom:7d44855bca. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 31 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winNOTEOct 31 2024
R-4.3-macNOTEOct 31 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.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtableHDF5ArrayhttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigR6RColorBrewerRcppRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalessnowSparseArraysparseMatrixStatsSummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc

Methrix tutorial

CompEpigen

Rendered frommethrix.Rmdusingknitr::rmarkdownon Oct 30 2024.

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