Package: rifi
Title: 'rifi' analyses data from rifampicin time series created by
        microarray or RNAseq
Version: 1.16.0
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
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev liblzma-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:58:25 UTC
RemoteUrl: https://github.com/bioc/rifi
RemoteRef: RELEASE_3_23
RemoteSha: d66cefb707e27a86c79e0622179fb43ddac809a1
NeedsCompilation: no
Packaged: 2026-04-30 06:10:59 UTC; root
Author: Loubna Youssar [aut, ctb],
  Walja Wanney [aut, ctb],
  Jens Georg [aut, cre]
Maintainer: Jens Georg <jens.georg@biologie.uni-freiburg.de>
Built: R 4.6.0; ; 2026-04-30 06:36:11 UTC; unix
