vmrseq
This is the released version of vmrseq; for the devel version, see vmrseq.
Probabilistic Modeling of Single-cell Methylation Heterogeneity
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DNAMethylation, Epigenetics, ImmunoOncology, Sequencing, SingleCell, Software, WholeGenome |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 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, 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_1.4.0.tar.gz |
| Windows Binary (x86_64) | vmrseq_1.4.0.zip |
| macOS Binary (big-sur-x86_64) | vmrseq_1.4.0.tgz |
| macOS Binary (sonoma-arm64) | vmrseq_1.4.0.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/ |
| Package Downloads Report | Download Stats |