iCOBRA
This is the development version of iCOBRA; for the stable release version, see iCOBRA.
Comparison and Visualization of Ranking and Assignment Methods
Bioconductor version: Development (3.24)
This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. Various types of performance plots can be generated programmatically. The package also contains a shiny application for interactive exploration of results.
Author: Charlotte Soneson [aut, cre]
Maintainer: Charlotte Soneson <charlottesoneson at gmail.com>
citation("iCOBRA")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("iCOBRA")
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("iCOBRA")| iCOBRA User Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, Software, Visualization |
| Version | 1.41.1 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 years) |
| License | GPL (>=2) |
| Depends | R (>= 4.4.0) |
| Imports | shiny (>= 0.9.1.9008), shinydashboard, reshape2, ggplot2 (>= 3.4.0), scales, ROCR, dplyr, DT, limma, methods, utils, rlang, prompter, SimpleUpset, patchwork |
| System Requirements | |
| URL | https://csoneson.github.io/iCOBRA/ |
| Bug Reports | https://github.com/csoneson/iCOBRA/issues |
See More
| Suggests | knitr, markdown, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | muscat |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | iCOBRA_1.41.1.tar.gz |
| Windows Binary (x86_64) | iCOBRA_1.41.1.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | iCOBRA_1.41.1.tgz |
| macOS Binary (sonoma-arm64) | iCOBRA_1.41.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/iCOBRA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/iCOBRA |
| Bioc Package Browser | https://code.bioconductor.org/browse/iCOBRA/ |
| Package Short Url | https://bioconductor.org/packages/iCOBRA/ |
| Package Downloads Report | Download Stats |