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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.
| Version: | 1.1.8 |
| Depends: | R (≥ 4.4) |
| Imports: | dplyr, parallel, tidyr, tidyselect, ggplot2, pracma, stats, ggrepel, matrixStats, rlang, magrittr, purrr, rtracklayer, GenomicRanges, GenomeInfoDb, valr, tibble, utils, methods |
| Suggests: | knitr, rmarkdown, testthat |
| Published: | 2025-04-22 |
| DOI: | 10.32614/CRAN.package.tepr |
| Author: | Nicolas Descostes [cre], Victor Billon [aut], Gael Cristofari [aut] |
| Maintainer: | Nicolas Descostes <nicolas.descostes at gmail.com> |
| License: | GPL-3 |
| NeedsCompilation: | no |
| Materials: | NEWS |
| CRAN checks: | tepr results |
| Reference manual: | tepr.pdf |
| Vignettes: |
Transcription Elongation Profiling (source, R code) |
| Package source: | tepr_1.1.8.tar.gz |
| Windows binaries: | r-devel: not available, r-release: tepr_1.1.8.zip, r-oldrel: tepr_1.1.8.zip |
| macOS binaries: | r-release (arm64): tepr_1.1.8.tgz, r-oldrel (arm64): tepr_1.1.8.tgz, r-release (x86_64): tepr_1.1.8.tgz, r-oldrel (x86_64): tepr_1.1.8.tgz |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.