{ "_id": "6a1feacbb401979e7343fe08", "Package": "tepr", "Title": "Transcription Elongation Profiling", "Version": "1.1.15", "Authors@R": "c(\nperson(\"Nicolas\", \"Descostes\", email = \"nicolas.descostes@gmail.com\", role = \"cre\"),\nperson(\"Victor\", \"Billon\", email = \"victor.billon@etu.univ-cotedazur.fr\", role = \"aut\"),\nperson(\"Gael\", \"Cristofari\", email = \"gael.cristofari@cnrs.fr\", role = \"aut\"))", "Description": "The general principle relies on calculating the cumulative\nsignal of nascent RNA sequencing over the gene body of any\ngiven gene or transcription unit. 'tepr' can identify\ntranscription attenuation sites by comparing profile to a null\nmodel which assumes uniform read density over the entirety of\nthe transcription unit. It can also identify increased or\ndiminished transcription attenuation by comparing two\nconditions. Besides rigorous statistical testing and high\nsensitivity, a major feature of 'tepr' is its ability to\nprovide the elongation pattern of each individual gene,\nincluding the position of the main attenuation point when such\na phenomenon occurs. Using 'tepr', users can visualize and\nrefine genome-wide aggregated analyses of elongation patterns\nto robustly identify effects specific to subsets of genes.\nThese metrics are suitable for internal comparisons (between\ngenes in each condition) and for studying elongation of the\nsame gene in different conditions or comparing it to a perfect\ntheoretical uniform elongation.", "Additional_repositories": "https://bioconductor.org/packages/3.22/bioc,\nhttps://bioconductor.org/packages/3.23/bioc", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Collate": "'allauc.R' 'attenuation.R' 'averageandfilterexprs.R'\n'countna.R' 'genesECDF.R' 'kneeid.R' 'meandifference.R'\n'plotauc.R' 'plotecdf.R' 'plothistoknee.R' 'plotmetagenes.R'\n'plotmulti.R' 'preprocessing-blacklisthighmap-utils.R'\n'preprocessing-blacklisthighmap.R'\n'preprocessing-createtablescores.R'\n'preprocessing-makewindows.R' 'preprocessing-retrieveanno.R'\n'preprocessing.R' 'tepr.R' 'universegroup.R' 'utils.R'", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libxml2-dev\nlibssl-dev libx11-dev xz-utils zlib1g-dev", "Repository": "https://descostesn.r-universe.dev", "Date/Publication": "2026-03-05 22:04:17 UTC", "RemoteUrl": "https://github.com/descostesn/tepr", "RemoteRef": "HEAD", "RemoteSha": "343005602d564bc29cca693f5199802a1e4c2c29", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-03 08:39:15 UTC", "User": "root" }, "Author": "Nicolas Descostes [cre],\nVictor Billon [aut],\nGael Cristofari [aut]", "Maintainer": "Nicolas Descostes ", "MD5sum": "c693f82822ee611613e6de1df36bb553", "_user": "descostesn", "_type": "src", "_file": "tepr_1.1.15.tar.gz", "_fileid": "cb42fb4501df30ad9ded7a227b712c5c149c8e9ed12d6afa21d4175114014bef", "_filesize": 4457495, "_sha256": "cb42fb4501df30ad9ded7a227b712c5c149c8e9ed12d6afa21d4175114014bef", "_created": "2026-06-03T08:39:15.000Z", "_published": "2026-06-03T08:50:19.062Z", "_distro": "noble", "_jobs": [ { 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