scmeth

DOI: 10.18129/B9.bioc.scmeth    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see scmeth.

Functions to conduct quality control analysis in methylation data

Bioconductor version: 3.11

Functions to analyze methylation data can be found here. Some functions are relevant for single cell methylation data but most other functions can be used for any methylation data. Highlight of this workflow is the comprehensive quality control report.

Author: Divy Kangeyan <divyswar01 at g.harvard.edu>

Maintainer: Divy Kangeyan <divyswar01 at g.harvard.edu>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("scmeth")

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("scmeth")

 

HTML	R Script	Vignette Title
PDF		Reference Manual
Text		NEWS

Details

biocViews	DNAMethylation, ImmunoOncology, Preprocessing, QualityControl, SingleCell, Software
Version	1.8.0
In Bioconductor since	BioC 3.7 (R-3.5) (2.5 years)
License	GPL-2
Depends	R (>= 3.5.0)
Imports	knitr, rmarkdown, bsseq, AnnotationHub, GenomicRanges, reshape2, stats, utils, BSgenome, DelayedArray(>= 0.5.15), annotatr, SummarizedExperiment(>= 1.5.6), GenomeInfoDb, Biostrings, DT, HDF5Array(>= 1.7.5)
LinkingTo
Suggests	BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, BiocGenerics, ggplot2, ggthemes
SystemRequirements
Enhances
URL
BugReports	https://github.com/aryeelab/scmeth/issues
Depends On Me
Imports Me
Suggests Me	biscuiteer
Links To Me
Build Report

Package Archives

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

Source Package	scmeth_1.8.0.tar.gz
Windows Binary	scmeth_1.8.0.zip
macOS 10.13 (High Sierra)	scmeth_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scmeth
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scmeth
Package Short Url	https://bioconductor.org/packages/scmeth/
Package Downloads Report	Download Stats