borealis

This is the released version of borealis; for the devel version, see borealis.

Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution

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DOI: 10.18129/B9.bioc.borealis

Bioconductor version: Release (3.22)

Borealis is an R library performing outlier analysis for count-based bisulfite sequencing data. It detectes outlier methylated CpG sites from bisulfite sequencing (BS-seq). The core of Borealis is modeling Beta-Binomial distributions. This can be useful for rare disease diagnoses.

Author: Garrett Jenkinson [aut, cre] ORCID iD ORCID: 0000-0003-2548-098X

Maintainer: Garrett Jenkinson <gargar934 at gmail.com>

Citation (from within R, enter citation("borealis")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("borealis")

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("borealis")

Borealis outlier methylation detection HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, DNAMethylation, DifferentialMethylation, Sequencing, Software

Version 1.14.0

In Bioconductor since BioC 3.15 (R-4.2) (3.5 years)

License GPL-3

Depends R (>= 4.2.0), Biobase

Imports doParallel, snow, purrr, plyr, foreach, gamlss, gamlss.dist, bsseq, methods, DSS, R.utils, utils, stats, ggplot2, cowplot, dplyr, rlang, GenomicRanges

System Requirements

URL

Suggests BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, annotatr, tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package borealis_1.14.0.tar.gz

Windows Binary (x86_64) borealis_1.14.0.zip

macOS Binary (x86_64) borealis_1.14.0.tgz

macOS Binary (arm64) borealis_1.14.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/borealis

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/borealis

Bioc Package Browser https://code.bioconductor.org/browse/borealis/

Package Short Url https://bioconductor.org/packages/borealis/

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