Package: borealis 1.16.0

Garrett Jenkinson

borealis: Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution

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.

Authors:Garrett Jenkinson [aut, cre]

borealis_1.16.0.tar.gz
borealis_1.16.0.zip(r-4.7)borealis_1.16.0.zip(r-4.6)borealis_1.16.0.zip(r-4.5)
borealis_1.16.0.tgz(r-4.6-any)borealis_1.16.0.tgz(r-4.5-any)
borealis_1.16.0.tar.gz(r-4.7-any)borealis_1.16.0.tar.gz(r-4.6-any)
borealis_1.16.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
borealis/json (API)
NEWS

# Install 'borealis' in R:

install.packages('borealis', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:borealis-1.17.0(bioc 3.24)borealis-1.16.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

sequencing coverage dnamethylation differentialmethylation

3.53 score 17 scripts 322 downloads 3 exports 107 dependencies

Last updated from:3fdced468c (on RELEASE_3_23). Checks:8 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	266
linux-devel-x86_64	NOTE	484
source / vignettes	OK	422
linux-release-x86_64	NOTE	508
macos-release-arm64	NOTE	268
macos-oldrel-arm64	NOTE	317
windows-devel	NOTE	391
windows-release	NOTE	348
windows-oldrel	NOTE	443
wasm-release	OK	208

Exports:plotCpGsite runBorealis runSingleNewSample

Dependencies:abind askpass assorthead beachmat BH Biobase BiocGenerics BiocIO biocmake BiocParallel Biostrings bitops BSgenome bsseq cigarillo cli codetools cowplot cpp11 crayon curl data.table DelayedArray DelayedMatrixStats dir.expiry doParallel dplyr DSS farver filelock foreach formatR futile.logger futile.options gamlss gamlss.data gamlss.dist generics GenomicAlignments GenomicRanges ggplot2 glue gtable gtools h5mread HDF5Array httr IRanges isoband iterators jsonlite labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mime nlme openssl permute pillar pkgconfig plyr purrr R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RCurl restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray sparseMatrixStats statmod SummarizedExperiment survival sys tibble tidyselect utf8 vctrs viridisLite withr XML XVector yaml

Borealis outlier methylation detection

Gavin Oliver, Garrett Jenkinson, Eric Klee

Rendered fromborealis.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2022-12-30
Started: 2022-03-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution	borealis-package borealis
Generate a plot of the model and raw data at one or more CpG sites	plotCpGsite
Run the full borealis pipeline	runBorealis
Run a single new sample after modeling complete	runSingleNewSample