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scmeth

Functions to conduct quality control analysis in methylation data

Bioconductor version: 3.23 · Package version: 1.32.0

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

MaintainerDivy Kangeyan <divyswar01@g.harvard.edu>
AuthorDivy Kangeyan <divyswar01@g.harvard.edu>
LicenseGPL-2
Bug Reportshttps://github.com/aryeelab/scmeth/issues
Downloads rank533
Source branchRELEASE_3_23
biocViewsDNAMethylation, ImmunoOncology, Preprocessing, QualityControl, SingleCell, Software

Documentation

Download

Follow the installation instructions to use this package in your R session.

Source packagescmeth_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

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