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>

Citation (from within R, enter citation("rifiComparative")):

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")
rifiComparative HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DifferentialExpression, GeneRegulation, Microarray, RNASeq, Software, Transcriptomics
Version 1.0.1
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
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
System Requirements
URL
Bug Reports https://github.com/CyanolabFreiburg/rifiComparative
See More
Suggests DescTools, devtools, knitr, rmarkdown, BiocStyle
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 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
Old Source Packages for BioC 3.17 Source Archive