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borealis

Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution


Bioconductor version: Release (3.18)

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 1.6.0
In Bioconductor since BioC 3.15 (R-4.2) (2 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
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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_1.6.0.tar.gz
Windows Binary borealis_1.6.0.zip
macOS Binary (x86_64) borealis_1.6.0.tgz
macOS Binary (arm64) borealis_1.6.0.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