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borealis

Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution

Bioconductor version: Release (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>

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

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

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
Linking To
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_1.4.0.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