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rifiComparative

This is the development version of rifiComparative; for the stable release version, see rifiComparative.

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


Bioconductor version: Development (3.19)

'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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.3.0
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, 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_1.3.0.tar.gz
Windows Binary
macOS Binary (x86_64) rifiComparative_1.3.0.tgz
macOS Binary (arm64) rifiComparative_1.3.0.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