Package: borealis 1.11.0

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]

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borealis.pdf |borealis.html✨
borealis/json (API)
NEWS

# Install 'borealis' in R:

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

On BioConductor:borealis-1.9.0(bioc 3.20)borealis-1.8.0(bioc 3.19)

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

sequencing coverage dnamethylation differentialmethylation

3.64 score 22 scripts 147 downloads 3 exports 108 dependencies

Last updated 23 days agofrom:9ec3feed7c. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 30 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	NOTE	Oct 30 2024
R-4.4-mac	NOTE	Oct 30 2024
R-4.3-win	NOTE	Oct 30 2024
R-4.3-mac	NOTE	Oct 30 2024

Exports:plotCpGsite runBorealis runSingleNewSample

Dependencies:abind askpass assorthead beachmat BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bitops BSgenome bsseq cli codetools colorspace cowplot cpp11 crayon curl data.table DelayedArray DelayedMatrixStats doParallel dplyr DSS fansi farver foreach formatR futile.logger futile.options gamlss gamlss.data gamlss.dist generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 glue gtable gtools HDF5Array httr IRanges isoband iterators jsonlite labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell 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 scales snow SparseArray sparseMatrixStats statmod SummarizedExperiment survival sys tibble tidyselect UCSC.utils utf8 vctrs viridisLite withr XML XVector yaml zlibbioc

Borealis outlier methylation detection

Gavin Oliver, Garrett Jenkinson, Eric Klee

Rendered fromborealis.Rmdusingknitr::rmarkdownon Oct 30 2024.

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