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biscuiteer

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

Convenience Functions for Biscuit

Bioconductor version: Development (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")

# 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")
Biscuiteer User Guide HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DNAMethylation, DataImport, MethylSeq, Software
Version 1.15.0
In Bioconductor since BioC 3.10 (R-3.6) (4 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
Linking To
Suggests DSS, covr, knitr, rmarkdown, markdown, rlang, scmeth, pkgdown, roxygen2, testthat, QDNAseq.hg19, QDNAseq.mm10, BiocStyle
System Requirements
Enhances
URL https://github.com/trichelab/biscuiteer
Bug Reports https://github.com/trichelab/biscuiteer/issues
See More
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_1.15.0.tar.gz
Windows Binary biscuiteer_1.15.0.zip
macOS Binary (x86_64) biscuiteer_1.15.0.tgz
macOS Binary (arm64)
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