scmeth
Functions to conduct quality control analysis in methylation data
Bioconductor version: 3.23 · Package version: 1.32.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scmeth")Details
| Maintainer | Divy Kangeyan <divyswar01@g.harvard.edu> |
| Author | Divy Kangeyan <divyswar01@g.harvard.edu> |
| License | GPL-2 |
| Bug Reports | https://github.com/aryeelab/scmeth/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNAMethylation, ImmunoOncology, Preprocessing, QualityControl, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/scmeth/ |
Citation
From within R, enter citation("scmeth"):
Divy Kangeyan. scmeth: Functions to conduct quality control analysis in methylation data. doi:10.18129/B9.bioc.scmeth, R package version 1.32.0, https://bioconductor.org/packages/scmeth.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | scmeth_1.32.0.tar.gz |
| Windows binary (x86_64) | scmeth_1.32.0.zip |
| macOS binary (arm64) | scmeth_1.32.0.tgz |
| macOS binary (x86_64) | scmeth_1.32.0.tgz |
Dependencies
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)
Suggests: knitr, rmarkdown, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, ggplot2, ggthemes
Reverse dependencies
Suggests Me (1): biscuiteer