Package: rifi
Title: 'rifi' analyses data from rifampicin time series created by
        microarray or RNAseq
Version: 1.13.0
Authors@R: c(person("Loubna", "Youssar", email = "lyoussar@gmail.com", role = c("aut", "ctb")), person("Walja", "Wanney", email = "jawalja@gmail.com", role = c("aut", "ctb")),person("Jens", "Georg", email = "jens.georg@biologie.uni-freiburg.de", role = c("aut", "cre")))
Description: '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.
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
Suggests: DescTools, devtools, knitr, rmarkdown, BiocStyle
VignetteBuilder: knitr
biocViews: RNASeq, DifferentialExpression, GeneRegulation,
        Transcriptomics, Regression, Microarray, Software
BugReports: https://github.com/CyanolabFreiburg/rifi
License: GPL-3 + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.12
Language: en-US
git_url: https://git.bioconductor.org/packages/rifi
git_branch: devel
git_last_commit: 9442274
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-04-27
NeedsCompilation: no
Packaged: 2025-04-27 21:22:58 UTC; biocbuild
Author: Loubna Youssar [aut, ctb],
  Walja Wanney [aut, ctb],
  Jens Georg [aut, cre]
Maintainer: Jens Georg <jens.georg@biologie.uni-freiburg.de>
Built: R 4.5.0; ; 2025-04-28 02:28:04 UTC; unix
