R Observatory: Metrics for TFMPvalue version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TFMPvalue

1.0.0

Efficient and Accurate P-Value Computation for Position Weight Matrices

0packages depend

56.2Kdownloads / year

0.7%test coverage

13/13checks pass

Overview

About

Maintained by Ge TanFirst published 2014-03-318 releasesCRAN page ↗GitHub ↗

In putative Transcription Factor Binding Sites (TFBSs) identification from sequence/alignments, we are interested in the significance of certain match score. TFMPvalue provides the accurate calculation of P-value with score threshold for Position Weight Matrices, or the score with given P-value. It is an interface to code originally made available by Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. doi:10.1186/1748-7188-2-15.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("ge11232002/TFMPvalue")

Development version from ge11232002/TFMPvalue. Installs pak first if it is not already available.

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-tfmpvalue

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-TFMPvalue

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-TFMPvalue

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 3.0 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.48

0.7%

Coverage · measured lines

100%

Documentation · exports

1

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 67%
Documented parameters: 52%
Return-value docs: 100%
References docs: 50%

Downloads

56.2K

CRAN downloads in the past year

Rank #1,876 · ~154/day · ~4.7K/mo

Releases R versions

Daily download trend is not available in this view yet.

3.8K30 days

11.5K90 days

56.2K1 year

Compare downloads with other packages →

Also on757 r2u22 autocran19.2K conda_forge213 bioconda7 c2d4u

Repository

GitHub ↗ ge11232002/tfmpvalue

2Stars

4Forks

3Open issues

1Open PRs

0Releases

54Commits

3Contributors

54 commits · Last activity 2026-01-18

Stars over time

2025-03-04 · 22026-07-07 · 2

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/ge11232002/tfmpvalue on 2026-08-16.

Continuous integration (1)

Travis CI

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.5.0

Imports (1)

Rcpp

LinkingTo (1)

Rcpp

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Ge Tan

Author, Maintainer

Authors (1)

Ge Tan

Author, Maintainer

Package Timeline

8 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.0Latest
2026-01-19 · current release · diff ↗
unarchivedReturned to CRAN
2026-01-19
archivedRemoved from CRAN
2025-12-25
issues were not addressed in time
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.0.9
2022-10-21 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
0.0.8
2018-05-16 · diff ↗
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03

Show 8 earlier events

0.0.6
2015-11-29 · diff ↗
R
R 3.2.0 released · 2015-04-16
0.0.5
2014-05-11 · diff ↗
0.0.4
2014-04-26 · diff ↗
0.0.3
2014-04-24 · diff ↗
R
R 3.1.0 released · 2014-04-10
0.0.2
2014-03-31
R
R 3.0.0 released · 2013-04-03

Package metadata

First published: 2014-03-31
Total releases: 8 / 12 yrs
License: GPL-2 OSI
Minimum R: ≥ 4.5.0
Download size: 15 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("TFMPvalue")

Format

Tan, G. (2026). TFMPvalue: Efficient and Accurate P-Value Computation for Position Weight Matrices (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.TFMPvalue

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 TFMPvalue version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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