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scmeth (development version)

scmeth

This is the development version of scmeth; for the stable release version, see scmeth.

Functions to conduct quality control analysis in methylation data

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DOI: 10.18129/B9.bioc.scmeth

Bioconductor version: Development (3.23)

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 "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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")

Vignette Title HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DNAMethylation, ImmunoOncology, Preprocessing, QualityControl, SingleCell, Software

Version 1.31.0

In Bioconductor since BioC 3.7 (R-3.5) (7.5 years)

License GPL-2

Depends R (>= 3.5.0)

Imports BiocGenerics, bsseq, AnnotationHub, Seqinfo, GenomicRanges, reshape2, stats, utils, BSgenome, DelayedArray(>= 0.5.15), annotatr, SummarizedExperiment(>= 1.5.6), GenomeInfoDb, Biostrings, DT, HDF5Array(>= 1.7.5)

System Requirements

URL

Bug Reports https://github.com/aryeelab/scmeth/issues

See More

Suggests knitr, rmarkdown, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, ggplot2, ggthemes

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Package Archives

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

Source Package scmeth_1.31.0.tar.gz

Windows Binary (x86_64) scmeth_1.31.0.zip

macOS Binary (x86_64)

macOS Binary (arm64)

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/

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