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biscuiteer

Convenience Functions for Biscuit


Bioconductor version: Release (3.18)

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 "4.3") 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

Details

biocViews DNAMethylation, DataImport, MethylSeq, Software
Version 1.16.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 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
See More
Suggests DSS, covr, knitr, rmarkdown, markdown, rlang, scmeth, pkgdown, roxygen2, testthat, QDNAseq.hg19, QDNAseq.mm10, BiocStyle
Linking To
Enhances
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Package Archives

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

Source Package biscuiteer_1.16.0.tar.gz
Windows Binary biscuiteer_1.16.0.zip (64-bit only)
macOS Binary (x86_64) biscuiteer_1.16.0.tgz
macOS Binary (arm64) biscuiteer_1.16.0.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/
Package Downloads Report Download Stats