Package: tepr
Title: Transcription Elongation Profiling
Version: 1.1.15
Authors@R: c(
    person("Nicolas", "Descostes", email = "nicolas.descostes@gmail.com", role = "cre"),
    person("Victor", "Billon", email = "victor.billon@etu.univ-cotedazur.fr", role = "aut"),
    person("Gael", "Cristofari", email = "gael.cristofari@cnrs.fr", role = "aut"))
Description: 
    The general principle relies on calculating the cumulative signal of nascent
    RNA sequencing over the gene body of any given gene or transcription unit.
    'tepr' can identify transcription attenuation sites by comparing profile to
    a null model which assumes uniform read density over the entirety of the
    transcription unit. It can also identify increased or diminished
    transcription attenuation by comparing two conditions. Besides rigorous
    statistical testing and high sensitivity, a major feature of 'tepr' is its
    ability to provide the elongation pattern of each individual gene, including
    the position of the main attenuation point when such a phenomenon occurs.
    Using 'tepr', users can visualize and refine genome-wide aggregated analyses
    of elongation patterns to robustly identify effects specific to subsets of
    genes. These metrics are suitable for internal comparisons (between genes in
    each condition) and for studying elongation of the same gene in different
    conditions or comparing it to a perfect theoretical uniform elongation. 
Depends: R (>= 4.4)
Additional_repositories: https://bioconductor.org/packages/3.22/bioc,
        https://bioconductor.org/packages/3.23/bioc
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Suggests: knitr, rmarkdown, testthat
Imports: dplyr, parallel, tidyr, tidyselect, ggplot2, pracma, stats,
        ggrepel, matrixStats, rlang, magrittr, purrr, rtracklayer,
        GenomicRanges, GenomeInfoDb, valr, tibble, utils, methods, MASS
Collate: 'allauc.R' 'attenuation.R' 'averageandfilterexprs.R'
        'countna.R' 'genesECDF.R' 'kneeid.R' 'meandifference.R'
        'plotauc.R' 'plotecdf.R' 'plothistoknee.R' 'plotmetagenes.R'
        'plotmulti.R' 'preprocessing-blacklisthighmap-utils.R'
        'preprocessing-blacklisthighmap.R'
        'preprocessing-createtablescores.R'
        'preprocessing-makewindows.R' 'preprocessing-retrieveanno.R'
        'preprocessing.R' 'tepr.R' 'universegroup.R' 'utils.R'
NeedsCompilation: no
Packaged: 2026-03-05 22:08:01 UTC; nxd1024
Author: Nicolas Descostes [cre],
  Victor Billon [aut],
  Gael Cristofari [aut]
Maintainer: Nicolas Descostes <nicolas.descostes@gmail.com>
Repository: CRAN
Date/Publication: 2026-03-06 10:20:02 UTC
Built: R 4.5.3; ; 2026-06-15 05:26:26 UTC; windows
