rifi

DOI: 10.18129/B9.bioc.rifi  

'rifi' analyses data from rifampicin time series created by microarray or RNAseq

Bioconductor version: Release (3.16)

'rifi' analyses data from rifampicin time series created by microarray or RNAseq. 'rifi' is a transcriptome data analysis tool for the holistic identification of transcription and decay associated processes. The decay constants and the delay of the onset of decay is fitted for each probe/bin. Subsequently, probes/bins of equal properties are combined into segments by dynamic programming, independent of a existing genome annotation. This allows to detect transcript segments of different stability or transcriptional events within one annotated gene. In addition to the classic decay constant/half-life analysis, 'rifi' detects processing sites, transcription pausing sites, internal transcription start sites in operons, sites of partial transcription termination in operons, identifies areas of likely transcriptional interference by the collision mechanism and gives an estimate of the transcription velocity. All data are integrated to give an estimate of continous transcriptional units, i.e. operons. Comprehensive output tables and visualizations of the full genome result and the individual fits for all probes/bins are produced.

Author: Loubna Youssar [aut, ctb], Walja Wanney [aut, ctb], Jens Georg [aut, cre]

Maintainer: Jens Georg <jens.georg at biologie.uni-freiburg.de>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("rifi")

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("rifi")

 

HTML	R Script	Rifi for decay estimation, based on high resolution microarray or RNA-seq data
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DifferentialExpression, GeneRegulation, Microarray, RNASeq, Regression, Software, Transcriptomics
Version	1.2.2
In Bioconductor since	BioC 3.15 (R-4.2) (1 year)
License	GPL-3 + file LICENSE
Depends	R (>= 4.2)
Imports	car, cowplot, doMC, parallel, dplyr, egg, foreach, ggplot2, graphics, grDevices, grid, methods, nls2, nnet, rlang, S4Vectors, scales, stats, stringr, SummarizedExperiment, tibble, rtracklayer, reshape2, utils
LinkingTo
Suggests	DescTools, knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL
BugReports	https://github.com/CyanolabFreiburg/rifi
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	rifi_1.2.2.tar.gz
Windows Binary
macOS Binary (x86_64)	rifi_1.2.2.tgz
macOS Binary (arm64)	rifi_1.2.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/rifi
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/rifi
Bioc Package Browser	https://code.bioconductor.org/browse/rifi/
Package Short Url	https://bioconductor.org/packages/rifi/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.16	Source Archive