Package: methylSig 1.17.0

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]

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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

Datasets:

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-1.17.0(bioc 3.20)methylSig-1.16.0(bioc 3.19)

bioconductor-package

9 exports 0.61 score 80 dependencies 11 mentions

Last updated 2 months agofrom:0003bd7e8c

Exports:diff_binomial diff_dss_fit diff_dss_test diff_methylsig filter_loci_by_coverage filter_loci_by_group_coverage filter_loci_by_location tile_by_regions tile_by_windows

Dependencies:abind askpass beachmat BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bitops BSgenome bsseq cli codetools colorspace cpp11 crayon curl data.table DelayedArray DelayedMatrixStats DSS farver formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges glue gtools HDF5Array httr IRanges jsonlite labeling lambda.r lattice lifecycle limma locfit Matrix MatrixGenerics matrixStats mime munsell openssl permute R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RCurl restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors scales snow SparseArray sparseMatrixStats statmod SummarizedExperiment sys UCSC.utils viridisLite XML XVector yaml zlibbioc

Updating methylSig code

Raymond G. Cavalcante

Rendered fromupdating-methylSig-code.Rmdusingknitr::rmarkdownon Jun 18 2024.

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

Using methylSig

Yongseok Park, Raymond G. Cavalcante, Maria E. Figueroa, Laura S. Rozek, and Maureen A. Sartor

Rendered fromusing-methylSig.Rmdusingknitr::rmarkdownon Jun 18 2024.

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

Citation

Development and contributors

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