vmrseq

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see vmrseq.

Probabilistic Modeling of Single-cell Methylation Heterogeneity

Bioconductor version: 3.21

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.

Author: Ning Shen [aut, cre]

Maintainer: Ning Shen <ning.shen.wk at gmail.com>

Citation (from within R, enter citation("vmrseq")):

Installation

To install this package, start R (version "4.5") and enter:


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

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("vmrseq")

Analyzing single-cell bisulfite sequencing data with vmrseq HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DNAMethylation, Epigenetics, ImmunoOncology, Sequencing, SingleCell, Software, WholeGenome

Version 1.0.1

In Bioconductor since BioC 3.21 (R-4.5) (0.5 years)

License MIT + file LICENSE

Depends R (>= 4.5.0)

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

System Requirements

URL https://github.com/nshen7/vmrseq

Bug Reports https://github.com/nshen7/vmrseq/issues

Suggests knitr, rmarkdown, testthat (>= 3.0.0)

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package vmrseq_1.0.1.tar.gz

Windows Binary (x86_64) vmrseq_1.0.1.zip

macOS Binary (x86_64) vmrseq_1.0.1.tgz

macOS Binary (arm64) vmrseq_1.0.1.tgz

Source Repository git clone https://git.bioconductor.org/packages/vmrseq

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/vmrseq

Bioc Package Browser https://code.bioconductor.org/browse/vmrseq/

Package Short Url https://bioconductor.org/packages/vmrseq/

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