biscuiteer

DOI: 10.18129/B9.bioc.biscuiteer    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see biscuiteer.

Convenience Functions for Biscuit

Bioconductor version: 3.12

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, Jr. [aut, cre], Wanding Zhou [aut], Ben Johnson [aut], Jacob Morrison [aut], Lyong Heo [aut]

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML	R Script	Biscuiteer User Guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	DNAMethylation, DataImport, MethylSeq, Software
Version	1.4.0
In Bioconductor since	BioC 3.10 (R-3.6) (1.5 years)
License	GPL-3
Depends	R (>= 3.6), biscuiteerData, bsseq
Imports	readr, qualV, Matrix, impute, HDF5Array, S4Vectors, Rsamtools, data.table, Biobase, GenomicRanges, BiocGenerics, VariantAnnotation, DelayedMatrixStats, SummarizedExperiment, GenomeInfoDb, Mus.musculus, Homo.sapiens, matrixStats, rtracklayer, QDNAseq, dmrseq, methods, utils, R.utils, gtools, BiocParallel
LinkingTo
Suggests	DSS, covr, knitr, rlang, scmeth, pkgdown, roxygen2, testthat, QDNAseq.hg19, QDNAseq.mm10
SystemRequirements
Enhances
URL	https://github.com/trichelab/biscuiteer
BugReports	https://github.com/trichelab/biscuiteer/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	biscuiteer_1.4.0.tar.gz
Windows Binary	biscuiteer_1.4.0.zip
macOS 10.13 (High Sierra)	biscuiteer_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/biscuiteer
Source Repository (Developer Access)	git clone [email protected]:packages/biscuiteer
Package Short Url	https://bioconductor.org/packages/biscuiteer/
Package Downloads Report	Download Stats