borealis
This is the released version of borealis; for the devel version, see borealis.
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]
Maintainer: Garrett Jenkinson <gargar934 at gmail.com>
citation("borealis")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | ||
| NEWS | Text |
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 |
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_1.16.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/borealis/ |
| Package Short Url | https://bioconductor.org/packages/borealis/ |
| Package Downloads Report | Download Stats |