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rifi

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

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


Bioconductor version: Development (3.19)

'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>

Citation (from within R, enter citation("rifi")):

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("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")
Rifi for decay estimation, based on high resolution microarray or RNA-seq data HTML R Script
Reference Manual PDF

Details

biocViews DifferentialExpression, GeneRegulation, Microarray, RNASeq, Regression, Software, Transcriptomics
Version 1.7.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
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
System Requirements
URL
Bug Reports https://github.com/CyanolabFreiburg/rifi
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Suggests DescTools, devtools, knitr, rmarkdown, BiocStyle
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Package Archives

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

Source Package rifi_1.7.0.tar.gz
Windows Binary
macOS Binary (x86_64) rifi_1.7.0.tgz
macOS Binary (arm64)
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