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("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 | ||
| 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 |