rifiComparative

DOI: 10.18129/B9.bioc.rifiComparative  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see rifiComparative.

'rifiComparative' compares the outputs of 'rifi' under two different conditions.

Bioconductor version: 3.17

'rifiComparative' is an extension of the 'rifi' package. It is designed to compare the outputs of 'rifi' under two different conditions by utilizing the half-life and mRNA at time 0 segments. To perform the segmentation, it takes into account the difference in half-life between the two conditions and the log2FC (fold change) of the mRNA at time 0. This package offers various functionalities such as segmentation, statistical analysis, summary tables, visualization of fragments, and additional plots that can be helpful for further analysis.

Author: Loubna Youssar [aut, cre], Jens cre Georg [aut]

Maintainer: Loubna Youssar <lyoussar at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("rifiComparative")

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("rifiComparative")

 

HTML	R Script	rifiComparative
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DifferentialExpression, GeneRegulation, Microarray, RNASeq, Software, Transcriptomics
Version	1.0.1
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	GPL-3 + file LICENSE
Depends	R (>= 4.2)
Imports	cowplot, doMC, parallel, dplyr, egg, foreach, ggplot2, ggrepel, graphics, grDevices, grid, methods, nnet, rlang, S4Vectors, scales, stats, stringr, tibble, rtracklayer, utils, writexl, DTA, LSD, reshape2, devtools, SummarizedExperiment
LinkingTo
Suggests	DescTools, devtools, knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL
BugReports	https://github.com/CyanolabFreiburg/rifiComparative
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	rifiComparative_1.0.1.tar.gz
Windows Binary
macOS Binary (x86_64)	rifiComparative_1.0.1.tgz
macOS Binary (arm64)	rifiComparative_1.0.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/rifiComparative
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/rifiComparative
Bioc Package Browser	https://code.bioconductor.org/browse/rifiComparative/
Package Short Url	https://bioconductor.org/packages/rifiComparative/
Package Downloads Report	Download Stats