SOMNiBUS
Smooth modeling of bisulfite sequencing
Bioconductor version: 3.23 · Package version: 1.20.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
This package aims to analyse count-based methylation data on predefined genomic regions, such as those obtained by targeted sequencing, and thus to identify differentially methylated regions (DMRs) that are associated with phenotypes or traits. The method is built a rich flexible model that allows for the effects, on the methylation levels, of multiple covariates to vary smoothly along genomic regions. At the same time, this method also allows for sequencing errors and can adjust for variability in cell type mixture.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SOMNiBUS")Details
| Maintainer | Kathleen Klein <kathleen.klein@mail.mcgill.ca> |
| Author | Kaiqiong Zhao [aut], Kathleen Klein [cre], Audrey Lemaçon [ctb, ctr], Simon Laurin-Lemay [ctb, ctr], My Intelligent Machines Inc. [ctr], Celia Greenwood [ths, aut] |
| License | MIT + file LICENSE |
| URL | https://github.com/kaiqiong/SOMNiBUS |
| Bug Reports | https://github.com/kaiqiong/SOMNiBUS/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNAMethylation, DifferentialMethylation, Epigenetics, FunctionalPrediction, Regression, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/SOMNiBUS/ |
Citation
From within R, enter citation("SOMNiBUS"):
Kaiqiong Zhao, Celia Greenwood. SOMNiBUS: Smooth modeling of bisulfite sequencing. doi:10.18129/B9.bioc.SOMNiBUS, R package version 1.20.0, https://bioconductor.org/packages/SOMNiBUS.
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 | SOMNiBUS_1.20.0.tar.gz |
| Windows binary (x86_64) | SOMNiBUS_1.20.0.zip |
| macOS binary (arm64) | SOMNiBUS_1.20.0.tgz |
| macOS binary (x86_64) | SOMNiBUS_1.20.0.tgz |
Dependencies
Depends: R (>= 4.1.0)
Imports: Matrix, mgcv, stats, VGAM, IRanges, GenomeInfoDb, GenomicRanges, rtracklayer, S4Vectors, BiocManager, annotatr, yaml, utils, bsseq, reshape2, data.table, ggplot2, tidyr
Suggests: BiocStyle, covr, devtools, dplyr, knitr, magick, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db