biscuiteer
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see biscuiteer.
Convenience Functions for Biscuit
Bioconductor version: 3.13
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>
citation("biscuiteer")
):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("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")
Biscuiteer User Guide | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | DNAMethylation, DataImport, MethylSeq, Software |
Version | 1.6.0 |
In Bioconductor since | BioC 3.10 (R-3.6) (4.5 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 |
System Requirements | |
URL | https://github.com/trichelab/biscuiteer |
Bug Reports | https://github.com/trichelab/biscuiteer/issues |
See More
Suggests | DSS, covr, knitr, rlang, scmeth, pkgdown, roxygen2, testthat, QDNAseq.hg19, QDNAseq.mm10 |
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.
Source Package | biscuiteer_1.6.0.tar.gz |
Windows Binary | biscuiteer_1.6.0.zip |
macOS 10.13 (High Sierra) | biscuiteer_1.6.0.tgz |
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 |
Old Source Packages for BioC 3.13 | Source Archive |