scmeth

DOI: 10.18129/B9.bioc.scmeth    

Functions to conduct quality control analysis in methylation data

Bioconductor version: Release (3.7)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("scmeth")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scmeth")

 

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Details

biocViews DNAMethylation, Preprocessing, QualityControl, SingleCell, Software
Version 1.0.1
License GPL-2
Depends R (>= 3.5.0)
Imports ggplot2, knitr, rmarkdown, bsseq, AnnotationHub, GenomicRanges, reshape2, stats, utils, BSgenome, DelayedArray(>= 0.5.15), annotatr, SummarizedExperiment(>= 1.5.6), GenomeInfoDb, Biostrings, DT, ggthemes, scales, viridis, 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
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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Source Package scmeth_1.0.1.tar.gz
Windows Binary scmeth_1.0.1.zip
Mac OS X 10.11 (El Capitan) scmeth_1.0.1.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 http://bioconductor.org/packages/scmeth/
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Old Source Packages for BioC 3.7 Source Archive

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