Package: tepr
Title: Transcription Elongation Profiling
Version: 1.1.16
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'
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libxml2-dev
        libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: https://descostesn.r-universe.dev
Date/Publication: 2026-07-02 19:43:22 UTC
RemoteUrl: https://github.com/descostesn/tepr
RemoteRef: HEAD
RemoteSha: a36062384217fe9f1c20fe8ac3189d25b1e1b29d
NeedsCompilation: no
Packaged: 2026-07-02 22:45:26 UTC; root
Author: Nicolas Descostes [cre],
  Victor Billon [aut],
  Gael Cristofari [aut]
Maintainer: Nicolas Descostes <nicolas.descostes@gmail.com>