biobroom
This package is for version 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see biobroom.
Turn Bioconductor objects into tidy data frames
Bioconductor version: Release (3.23)
This package contains methods for converting standard objects constructed by bioinformatics packages, especially those in Bioconductor, and converting them to tidy data. It thus serves as a complement to the broom package, and follows the same the tidy, augment, glance division of tidying methods. Tidying data makes it easy to recombine, reshape and visualize bioinformatics analyses.
Author: Andrew J. Bass, David G. Robinson, Steve Lianoglou, Emily Nelson, John D. Storey, with contributions from Laurent Gatto
Maintainer: John D. Storey <jstorey at princeton.edu> and Andrew J. Bass <ajbass at emory.edu>
citation("biobroom")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("biobroom")
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("biobroom")| Vignette Title | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, DifferentialExpression, GeneExpression, MultipleComparison, Proteomics, Regression, Software |
| Version | 1.43.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (11 years) |
| License | LGPL |
| Depends | R (>= 3.0.0), broom |
| Imports | dplyr, tidyr, Biobase |
| System Requirements | |
| URL | https://github.com/StoreyLab/biobroom |
| Bug Reports | https://github.com/StoreyLab/biobroom/issues |
See More
| Suggests | limma, DESeq2, airway, ggplot2, plyr, GenomicRanges, testthat, magrittr, edgeR, qvalue, knitr, data.table, MSnbase, rmarkdown, SummarizedExperiment |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | TPP |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | biobroom_1.43.0.tar.gz |
| Windows Binary (x86_64) | biobroom_1.43.0.zip |
| macOS Binary (big-sur-x86_64) | biobroom_1.43.0.tgz |
| macOS Binary (sonoma-arm64) | biobroom_1.43.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/biobroom |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/biobroom |
| Bioc Package Browser | https://code.bioconductor.org/browse/biobroom/ |
| Package Short Url | https://bioconductor.org/packages/biobroom/ |
| Package Downloads Report | Download Stats |