R Observatory: Metrics for tepr version 1.1.17

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

tepr

1.1.17Package record

Transcription Elongation Profiling

0packages depend

4.5Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Nicolas DescostesCRAN page ↗

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.

Changes in 1.1.17

Remove Additional_repositories from DESCRIPTION.

From NEWS in the release

Install

R (CRAN)Ubuntu (r2u)

install.packages("tepr", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-tepr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 11.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-10-01
ERROR12 OK, 1 ERROR2026-09-24
OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-24

Show 12 earlier changesHide 12 earlier changes

ERROR11 OK, 1 NOTE, 1 ERROR2026-06-19
NOTE12 OK, 1 NOTE2026-06-17
OK13 OK2026-06-14
ERROR11 OK, 2 ERROR2026-06-07
OK13 OK2026-06-03
ERROR11 OK, 2 ERROR2026-05-30
OK13 OK2026-05-10
ERROR12 OK, 1 ERROR2026-05-03
OK13 OK2026-05-01
ERROR12 OK, 1 ERROR2026-04-28
OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.17

READMENoVignettesYes · 1 · dynamicNEWSYes · 33% structured · mentions 1.1.17Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 24
Examples that run: 75%18 run in a plain check · 4 only when donttest examples are enabled (R CMD check --as-cran) · 2 never run
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Transcription Elongation Profiling

How these are measured

Downloads

4.5K

CRAN downloads in the past year

Rank #11,660 · ~12/day · ~371/mo

Releases R versions

Daily download trend is not available in this view yet.

40830 days

93590 days

4.5K1 year

Compare downloads with other packages →

Also on161 r2u

How downloads are counted

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing tepr adds 47 packages (26 with compiled code, 34 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, Rcpp 1.8 MB. 5 more not on CRAN are not measured.

Depends (1)

R >= 4.4

Imports (20)

dplyrparalleltidyr tidyselect ggplot2 pracmastatsggrepel matrixStats rlang magrittr purrr rtracklayer GenomicRanges GenomeInfoDb valr tibbleutilsmethodsMASS

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Nicolas Descostes

Maintainer since 1.1.8 (2025)

Victor Billon

Author

Gael Cristofari

Author

Releases (9)

Pick two releases to compare their code metrics.

1.1.17Latest
record
2026-07-08 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.1.15
record
2026-03-06 · diff ↗
1.1.14
record
2026-01-28 · diff ↗
1.1.13
record
2025-12-12 · diff ↗
1.1.12
record
2025-11-04 · diff ↗
1.1.11
record
2025-10-24 · diff ↗
1.1.10
record
2025-09-03 · diff ↗
unarchivedReturned to CRAN
2025-08-19
1.1.9
record
2025-08-19 · diff ↗ ·
added 1 export
retrievechrom
archivedRemoved from CRAN
2025-08-18
multiple policy violations On Internet access Repeatedly spamming personal addresses of team member in HTML
1.1.8
record
2025-04-22
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-04-22
Total releases: 9 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.4
Download size: 3.5 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("tepr")

Format

Descostes, N., Billon, V., & Cristofari, G. (2026). tepr: Transcription Elongation Profiling (Version 1.1.17) [Computer software]. https://doi.org/10.32614/CRAN.package.tepr

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for tepr version 1.1.17 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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