scmeth

DOI: 10.18129/B9.bioc.scmeth  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see scmeth.

Functions to conduct quality control analysis in methylation data

Bioconductor version: 3.17

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>

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

Installation

To install this package, start R (version "4.3") and enter:

if (!require("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 1.20.0
In Bioconductor since BioC 3.7 (R-3.5) (5.5 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_1.20.0.tar.gz
Windows Binary scmeth_1.20.0.zip (64-bit only)
macOS Binary (x86_64) scmeth_1.20.0.tgz
macOS Binary (arm64) scmeth_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scmeth
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scmeth
Bioc Package Browser https://code.bioconductor.org/browse/scmeth/
Package Short Url https://bioconductor.org/packages/scmeth/
Package Downloads Report Download Stats

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