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 (3.21)
'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("rifiComparative")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GeneRegulation, Microarray, RNASeq, Software, Transcriptomics |
| Version | 1.7.0 |
| 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 |
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_1.7.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |