Package: borealis 1.17.0

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_1.17.0.tar.gz
borealis_1.17.0.zip(r-4.7)borealis_1.17.0.zip(r-4.6)borealis_1.17.0.zip(r-4.5)
borealis_1.17.0.tgz(r-4.6-any)borealis_1.17.0.tgz(r-4.5-any)
borealis_1.17.0.tar.gz(r-4.7-any)borealis_1.17.0.tar.gz(r-4.6-any)
borealis_1.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
borealis/json (API)

# Install 'borealis' in R:

install.packages('borealis', repos = c('https://bioc.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

2.56 score 18 scripts 3 exports 108 dependencies

Last updated from:7bbd4fbc10. Checks:1 NOTE, 7 WARNING, 1 ERROR, 1 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	273
linux-devel-x86_64	WARNING	491
source / vignettes	ERROR	422
linux-release-x86_64	WARNING	527
macos-release-arm64	WARNING	296
macos-oldrel-arm64	WARNING	295
windows-devel	WARNING	344
windows-release	WARNING	365
windows-oldrel	WARNING	380
wasm-release	OK	245

Exports:plotCpGsite runBorealis runSingleNewSample

Dependencies:abind askpass assorthead beachmat BH Biobase BiocBaseUtils 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

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

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

Package: borealis 1.17.0

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

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