rifiComparative

'rifiComparative' compares the output of rifi from two different conditions.

Bioconductor version: Release (3.20)

'rifiComparative' is a continuation of rifi package. It compares two conditions output of rifi using half-life and mRNA at time 0 segments. As an input for the segmentation, the difference between half-life of both condtions and log2FC of the mRNA at time 0 are used. The package provides segmentation, statistics, summary table, fragments visualization and some additional useful plots for further anaylsis.

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 "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, GeneRegulation, Microarray, RNASeq, Software, Transcriptomics
Version	1.6.0
In Bioconductor since	BioC 3.17 (R-4.3) (1.5 years)
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

Suggests	DescTools, 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_1.6.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)	rifiComparative_1.6.0.tgz
macOS Binary (arm64)	rifiComparative_1.6.0.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