divergence
This is the released version of divergence; for the devel version, see divergence.
Divergence: Functionality for assessing omics data by divergence with respect to a baseline
Bioconductor version: Release (3.23)
This package provides functionality for performing divergence analysis as presented in Dinalankara et al, "Digitizing omics profiles by divergence from a baseline", PANS 2018. This allows the user to simplify high dimensional omics data into a binary or ternary format which encapsulates how the data is divergent from a specified baseline group with the same univariate or multivariate features.
Author: Wikum Dinalankara <wdd4001 at med.cornell.edu>, Luigi Marchionni <marchion at jhu.edu>, Qian Ke <qke1 at jhu.edu>
Maintainer: Wikum Dinalankara <wdd4001 at med.cornell.edu>, Luigi Marchionni <marchion at jhu.edu>
citation("divergence")):
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("divergence")
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("divergence")| Performing Divergence Analysis | HTML | R Script |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | Software, StatisticalMethod |
| Version | 1.28.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 years) |
| License | GPL-2 |
| Depends | R (>= 3.6), SummarizedExperiment |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown |
| 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 | divergence_1.28.0.tar.gz |
| Windows Binary (x86_64) | divergence_1.28.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | divergence_1.28.0.tgz |
| macOS Binary (sonoma-arm64) | divergence_1.28.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/divergence |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/divergence |
| Bioc Package Browser | https://code.bioconductor.org/browse/divergence/ |
| Package Short Url | https://bioconductor.org/packages/divergence/ |
| Package Downloads Report | Download Stats |