Package: methylSig 1.25.0

Raymond G. Cavalcante

methylSig: MethylSig: Differential Methylation Testing for WGBS and RRBS Data

MethylSig is a package for testing for differentially methylated cytosines (DMCs) or regions (DMRs) in whole-genome bisulfite sequencing (WGBS) or reduced representation bisulfite sequencing (RRBS) experiments. MethylSig uses a beta binomial model to test for significant differences between groups of samples. Several options exist for either site-specific or sliding window tests, and variance estimation.

Authors:Yongseok Park [aut], Raymond G. Cavalcante [aut, cre]

methylSig_1.25.0.tar.gz
methylSig_1.25.0.zip(r-4.7)methylSig_1.25.0.zip(r-4.6)methylSig_1.25.0.zip(r-4.5)
methylSig_1.25.0.tgz(r-4.6-any)methylSig_1.25.0.tgz(r-4.5-any)
methylSig_1.25.0.tar.gz(r-4.7-any)methylSig_1.25.0.tar.gz(r-4.6-any)
methylSig_1.25.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
methylSig/json (API)

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

Bug tracker:https://github.com/sartorlab/methylsig/issues

Datasets:

On BioConductor:methylSig-1.25.0(bioc 3.24)methylSig-1.24.0(bioc 3.23)

dnamethylationdifferentialmethylationepigeneticsregressionmethylseqdifferential-methylationdna-methylation

7.96 score 20 stars 38 scripts 11 mentions 9 exports 83 dependencies

Last updated from:3cf80514e4. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE260
linux-devel-x86_64OK508
source / vignettesOK358
linux-release-x86_64OK507
macos-release-arm64OK313
macos-oldrel-arm64OK233
windows-develOK432
windows-releaseOK462
windows-oldrelOK396
wasm-releaseOK237

Exports:diff_binomialdiff_dss_fitdiff_dss_testdiff_methylsigfilter_loci_by_coveragefilter_loci_by_group_coveragefilter_loci_by_locationtile_by_regionstile_by_windows

Dependencies:abindaskpassassortheadbeachmatBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocParallelBiostringsbitopsBSgenomebsseqcigarilloclicodetoolscpp11crayoncurldata.tableDelayedArrayDelayedMatrixStatsdir.expiryDSSfarverfilelockformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluegtoolsh5mreadHDF5ArrayhttrIRangesjsonlitelabelinglambda.rlatticelifecyclelimmalocfitMatrixMatrixGenericsmatrixStatsmimeopensslpermuteR.methodsS3R.ooR.utilsR6RColorBrewerRcppRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalesSeqinfosnowSparseArraysparseMatrixStatsstatmodSummarizedExperimentsysviridisLiteXMLXVectoryaml

Updating methylSig code
Introduction | Reading Data | Old methylSig | New methylSig | Tiling Data | Testing | MethylSig Test | DSS Test | Session Info
Rendered fromupdating-methylSig-code.Rmdusingknitr::rmarkdown

Last update: 2020-03-23
Started: 2020-03-23

Using methylSig
Introduction | Installation | Usage | Reading Data | Filtering Data | By Coverage | By Location | Aggregating Data | By Tiling the Genome | By Pre-defined Regions | Testing for Differential Methylation | Filtering by Coverage in a Minimum Number of Samples | Binomial Test | MethylSig Test | General Models with DSS | Model Fitting | Building Contrasts | Testing | Session Info
Rendered fromusing-methylSig.Rmdusingknitr::rmarkdown

Last update: 2020-03-23
Started: 2020-03-23