borealis

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15

Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution

Bioconductor version: Release (3.23)

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: 0000-0003-2548-098X

Maintainer: Garrett Jenkinson <gargar934 at gmail.com>

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

Garrett Jenkinson. borealis: Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution. doi:10.18129/B9.bioc.borealis, R package version 1.16.0, https://bioconductor.org/packages/borealis.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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	1.16.0
In Bioconductor since	BioC 3.15 (R-4.2) (4.5 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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	borealis_1.16.0.tar.gz
Windows Binary (x86_64)	borealis_1.16.0.zip
macOS Binary (big-sur-x86_64)	borealis_1.16.0.tgz
macOS Binary (sonoma-arm64)	borealis_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/borealis
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/borealis
Package Short Url	https://bioconductor.org/packages/borealis/
Package Downloads Report	Download Stats