vmrseq
This is the development version of vmrseq; for the stable release version, see vmrseq.
Probabilistic Modeling of Single-cell Methylation Heterogeneity
Bioconductor version: Development (3.22)
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("vmrseq")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DNAMethylation, Epigenetics, ImmunoOncology, Sequencing, SingleCell, Software, WholeGenome |
| Version | 1.1.1 |
| In Bioconductor since | BioC 3.21 (R-4.5) (< 6 months) |
| 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, devtools |
| System Requirements | |
| URL | https://github.com/nshen7/vmrseq |
| Bug Reports | https://github.com/nshen7/vmrseq/issues |
See More
| Suggests | knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | vmrseq_1.1.1.tar.gz |
| Windows Binary (x86_64) | vmrseq_1.1.1.zip (64-bit only) |
| macOS Binary (x86_64) | vmrseq_1.1.1.tgz |
| macOS Binary (arm64) | |
| 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/ |
| Package Downloads Report | Download Stats |