biscuiteer

This is the released version of biscuiteer; for the devel version, see biscuiteer.

Convenience Functions for Biscuit

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DOI: 10.18129/B9.bioc.biscuiteer

Bioconductor version: Release (3.22)

A test harness for bsseq loading of Biscuit output, summarization of WGBS data over defined regions and in mappable samples, with or without imputation, dropping of mostly-NA rows, age estimates, etc.

Author: Tim Triche [aut], Wanding Zhou [aut], Benjamin Johnson [aut], Jacob Morrison [aut, cre], Lyong Heo [aut], James Eapen [aut]

Maintainer: Jacob Morrison <jacob.morrison at vai.org>

Citation (from within R, enter citation("biscuiteer")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("biscuiteer")

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("biscuiteer")

Biscuiteer User Guide HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DNAMethylation, DataImport, MethylSeq, Software

Version 1.24.0

In Bioconductor since BioC 3.10 (R-3.6) (6 years)

License GPL-3

Depends R (>= 4.1.0), biscuiteerData, bsseq

Imports readr, qualV, Matrix, impute, HDF5Array, S4Vectors, Rsamtools, data.table, Biobase, GenomicRanges, IRanges, BiocGenerics, VariantAnnotation, DelayedMatrixStats, SummarizedExperiment, GenomeInfoDb, Mus.musculus, Homo.sapiens, matrixStats, rtracklayer, QDNAseq, dmrseq, methods, utils, R.utils, gtools, BiocParallel

System Requirements

URL https://github.com/trichelab/biscuiteer

Bug Reports https://github.com/trichelab/biscuiteer/issues

Suggests DSS, covr, knitr, rmarkdown, markdown, rlang, scmeth, pkgdown, roxygen2, testthat, QDNAseq.hg19, QDNAseq.mm10, BiocStyle

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package biscuiteer_1.24.0.tar.gz

Windows Binary (x86_64) biscuiteer_1.23.0.zip

macOS Binary (x86_64) biscuiteer_1.24.0.tgz

macOS Binary (arm64) biscuiteer_1.24.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/biscuiteer

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/biscuiteer

Bioc Package Browser https://code.bioconductor.org/browse/biscuiteer/

Package Short Url https://bioconductor.org/packages/biscuiteer/

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