biscuiteer
Convenience Functions for Biscuit
Bioconductor version: Release (3.20)
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("biscuiteer")):
Installation
To install this package, start R (version "4.4") 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 | 1.20.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (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.
| Source Package | biscuiteer_1.20.0.tar.gz |
| Windows Binary (x86_64) | biscuiteer_1.20.0.zip (64-bit only) |
| macOS Binary (x86_64) | biscuiteer_1.20.0.tgz |
| macOS Binary (arm64) | biscuiteer_1.20.0.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 |