Package: methylSig 1.19.0
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:
methylSig_1.19.0.tar.gz
methylSig_1.19.0.zip(r-4.5)methylSig_1.19.0.zip(r-4.4)methylSig_1.19.0.zip(r-4.3)
methylSig_1.19.0.tgz(r-4.4-any)methylSig_1.19.0.tgz(r-4.3-any)
methylSig_1.19.0.tar.gz(r-4.5-noble)methylSig_1.19.0.tar.gz(r-4.4-noble)
methylSig_1.19.0.tgz(r-4.4-emscripten)methylSig_1.19.0.tgz(r-4.3-emscripten)
methylSig.pdf |methylSig.html✨
methylSig/json (API)
NEWS
| # 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
- bsseq_destranded - BSseq object read from destranded coverage files
- bsseq_multichrom - BSseq object with loci on multiple chromosomes
- bsseq_stranded - BSseq object read from stranded coverage files
- promoters_gr - GRanges object with collapsed promoters on chr21 and chr22
On BioConductor:methylSig-1.19.0(bioc 3.21)methylSig-1.18.0(bioc 3.20)
dnamethylationdifferentialmethylationepigeneticsregressionmethylseqdifferential-methylationdna-methylation
Last updated 2 months agofrom:30882782fb. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | OK | Nov 29 2024 |
| R-4.5-linux | OK | Nov 29 2024 |
| R-4.4-win | OK | Nov 29 2024 |
| R-4.4-mac | OK | Nov 29 2024 |
| R-4.3-win | OK | Nov 29 2024 |
| R-4.3-mac | OK | Nov 29 2024 |
Exports:diff_binomialdiff_dss_fitdiff_dss_testdiff_methylsigfilter_loci_by_coveragefilter_loci_by_group_coveragefilter_loci_by_locationtile_by_regionstile_by_windows
Dependencies:abindaskpassassortheadbeachmatBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomebsseqclicodetoolscolorspacecpp11crayoncurldata.tableDelayedArrayDelayedMatrixStatsDSSfarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluegtoolsHDF5ArrayhttrIRangesjsonlitelabelinglambda.rlatticelifecyclelimmalocfitMatrixMatrixGenericsmatrixStatsmimemunsellopensslpermuteR.methodsS3R.ooR.utilsR6RColorBrewerRcppRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalessnowSparseArraysparseMatrixStatsstatmodSummarizedExperimentsysUCSC.utilsviridisLiteXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| BSseq object read from destranded coverage files | bsseq_destranded |
| BSseq object with loci on multiple chromosomes | bsseq_multichrom |
| BSseq object read from stranded coverage files | bsseq_stranded |
| Differential methylation analysis using binomial model | diff_binomial |
| Performs model fit for general experimental design | diff_dss_fit |
| Calculates differential methylation statistics under general experimental design | diff_dss_test |
| Calculates differential methylation statistics using a Beta-binomial approach | diff_methylsig |
| Filter BSseq object by coverage | filter_loci_by_coverage |
| Filter loci based on coverage threshold per sample per group | filter_loci_by_group_coverage |
| Remove loci by overlap with a 'GRanges' object | filter_loci_by_location |
| GRanges object with collapsed promoters on chr21 and chr22 | promoters_gr |
| Group cytosine / CpG level data into regions based on genomic regions | tile_by_regions |
| Group cytosine / CpG level data into regions based on genomic windows | tile_by_windows |
