biscuiteer

DOI: 10.18129/B9.bioc.biscuiteer    

This is the development version of biscuiteer; for the stable release version, see biscuiteer.

Convenience Functions for Biscuit

Bioconductor version: Development (3.11)

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: "Tim Triche, Jr." <tim.triche at gmail.com>

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

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.0
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
License GPL-3
Depends R (>= 3.6.0), 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
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_1.1.0.tar.gz
Windows Binary biscuiteer_1.1.0.zip
Mac OS X 10.11 (El Capitan) biscuiteer_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/biscuiteer
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/biscuiteer
Package Short Url https://bioconductor.org/packages/biscuiteer/
Package Downloads Report Download Stats

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