scmeth
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see scmeth.
Functions to conduct quality control analysis in methylation data
Bioconductor version: 3.9
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("scmeth")):
Installation
To install this package, start R (version "3.6") 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")| Vignette Title | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, ImmunoOncology, Preprocessing, QualityControl, SingleCell, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6 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) |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/aryeelab/scmeth/issues |
See More
| Suggests | BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, BiocGenerics, ggplot2, ggthemes |
| 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 | scmeth_1.4.0.tar.gz |
| Windows Binary | scmeth_1.4.0.zip |
| Mac OS X 10.11 (El Capitan) | scmeth_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scmeth |
| Source Repository (Developer Access) | git clone [email protected]:packages/scmeth |
| Bioc Package Browser | https://code.bioconductor.org/browse/scmeth/ |
| Package Short Url | https://bioconductor.org/packages/scmeth/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |