borealis
This is the development version of borealis; for the stable release version, see borealis.
Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution
Bioconductor version: Development (3.21)
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:
Maintainer: Garrett Jenkinson <gargar934 at gmail.com>
citation("borealis")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | ||
| NEWS | Text |
Details
| biocViews | Coverage, DNAMethylation, DifferentialMethylation, Sequencing, Software |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2.5 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 |
See More
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | borealis_1.11.0.tar.gz |
| Windows Binary (x86_64) | borealis_1.11.0.zip |
| macOS Binary (x86_64) | borealis_1.11.0.tgz |
| macOS Binary (arm64) | |
| 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 |