matchBox
This is the released version of matchBox; for the devel version, see matchBox.
Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis.
Bioconductor version: Release (3.23)
The matchBox package enables comparing ranked vectors of features, merging multiple datasets, removing redundant features, using CAT-plots and Venn diagrams, and computing statistical significance.
Author: Luigi Marchionni <marchion at jhu.edu>, Anuj Gupta <agupta52 at jhu.edu>
Maintainer: Luigi Marchionni <marchion at jhu.edu>, Anuj Gupta <agupta52 at jhu.edu>
citation("matchBox")):
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("matchBox")
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("matchBox")| Working with the matchBox package | R Script | |
| Reference Manual |
Details
| biocViews | Annotation, Microarray, MultipleComparison, Software, Visualization |
| Version | 1.54.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (14 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.8.0) |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | matchBox_1.54.0.tar.gz |
| Windows Binary (x86_64) | matchBox_1.54.0.zip |
| macOS Binary (big-sur-x86_64) | matchBox_1.54.0.tgz |
| macOS Binary (sonoma-arm64) | matchBox_1.54.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/matchBox |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/matchBox |
| Bioc Package Browser | https://code.bioconductor.org/browse/matchBox/ |
| Package Short Url | https://bioconductor.org/packages/matchBox/ |
| Package Downloads Report | Download Stats |