borealis

DOI: 10.18129/B9.bioc.borealis  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see borealis.

Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution

Bioconductor version: 3.17

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]

Maintainer: Garrett Jenkinson <gargar934 at gmail.com>

Installation

To install this package, start R (version "4.3") 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")

 

HTML	R Script	Borealis outlier methylation detection
PDF		Reference Manual
Text		NEWS

Details

biocViews	Coverage, DNAMethylation, DifferentialMethylation, Sequencing, Software
Version	1.4.0
In Bioconductor since	BioC 3.15 (R-4.2) (1.5 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
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, annotatr, tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	borealis_1.4.0.tar.gz
Windows Binary	borealis_1.4.0.zip
macOS Binary (x86_64)	borealis_1.4.0.tgz
macOS Binary (arm64)	borealis_1.4.0.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/
Package Downloads Report	Download Stats