biscuiteer

Convenience Functions for Biscuit

Bioconductor version: 3.23 · Package version: 1.26.0

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.

Installation

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

BiocManager::install("biscuiteer")

Details

Maintainer	Jacob Morrison <jacob.morrison@vai.org>
Author	Tim Triche [aut], Wanding Zhou [aut], Benjamin Johnson [aut], Jacob Morrison [aut, cre], Lyong Heo [aut], James Eapen [aut]
License	GPL-3
URL	https://github.com/trichelab/biscuiteer
Bug Reports	https://github.com/trichelab/biscuiteer/issues
Downloads rank	343
Source branch	RELEASE_3_23
biocViews	DNAMethylation, DataImport, MethylSeq, Software

Documentation

Biscuiteer User Guide

Download

Source package

Dependencies

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

Suggests: covr, knitr, rmarkdown, markdown, rlang, scmeth, pkgdown, roxygen2, testthat, QDNAseq.hg19, QDNAseq.mm10, BiocStyle