rifiComparative
This is the released version of rifiComparative; for the devel version, see rifiComparative.
'rifiComparative' compares the output of rifi from two different conditions.
Bioconductor version: Release (3.23)
'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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.12.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 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_1.12.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | rifiComparative_1.12.0.tgz |
| macOS Binary (sonoma-arm64) | rifiComparative_1.12.0.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 |