vmrseq

Probabilistic Modeling of Single-cell Methylation Heterogeneity

Bioconductor version: 3.23 · Package version: 1.4.0

High-throughput single-cell measurements of DNA methylation allows studying inter-cellular epigenetic heterogeneity, but this task faces the challenges of sparsity and noise. We present vmrseq, a statistical method that overcomes these challenges and identifies variably methylated regions accurately and robustly.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("vmrseq")

Details

Maintainer	Ning Shen <ning.shen.wk@gmail.com>
Author	Ning Shen [aut, cre]
License	MIT + file LICENSE
URL	https://github.com/nshen7/vmrseq
Bug Reports	https://github.com/nshen7/vmrseq/issues
Downloads rank	164
Source branch	RELEASE_3_23
biocViews	DNAMethylation, Epigenetics, ImmunoOncology, Sequencing, SingleCell, Software, WholeGenome

Documentation

Analyzing single-cell bisulfite sequencing data with vmrseq

Download

Source package

Dependencies

Depends: R (>= 4.5.0)

Imports: bumphunter, dplyr, BiocParallel, DelayedArray, GenomicRanges, ggplot2, methods, tidyr, locfit, gamlss.dist, recommenderlab, HDF5Array, data.table, SummarizedExperiment, IRanges, S4Vectors, devtools

Suggests: knitr, rmarkdown, testthat (>= 3.0.0)