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Bioconductor - biscuiteer (development version)

biscuiteer

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

Convenience Functions for Biscuit

Bioconductor version: Development (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")

# 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")
Details biocViews DNAMethylation, DataImport, MethylSeq, Software Version 1.23.0 In Bioconductor since BioC 3.10 (R-3.6) (5.5 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 Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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