R Observatory: Metrics for TransProR version 1.0.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TransProR

1.0.7

Analysis and Visualization of Multi-Omics Data

0packages depend

5.5Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Dongyue YuFirst published 2024-12-106 releasesCRAN page ↗GitHub ↗

A tool for comprehensive transcriptomic data analysis, with a focus on transcript-level data preprocessing, expression profiling, differential expression analysis, and functional enrichment. It enables researchers to identify key biological processes, disease biomarkers, and gene regulatory mechanisms. 'TransProR' is aimed at researchers and bioinformaticians working with RNA-Seq data, providing an intuitive framework for in-depth analysis and visualization of transcriptomic datasets. The package includes comprehensive documentation and usage examples to guide users through the entire analysis pipeline. The differential expression analysis methods incorporated in the package include 'limma' (Ritchie et al., 2015, doi:10.1093/nar/gkv007; Smyth, 2005, doi:10.1007/0-387-29362-0_23), 'edgeR' (Robinson et al., 2010, doi:10.1093/bioinformatics/btp616), 'DESeq2' (Love et al., 2014, doi:10.1186/s13059-014-0550-8), and Wilcoxon tests (Li et al., 2022, doi:10.1186/s13059-022-02648-4), providing flexible and robust approaches to RNA-Seq data analysis. For more information, refer to the package vignettes and related publications.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("TransProR", 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("SSSYDYSSS/TransProRBook")

Development version from SSSYDYSSS/TransProRBook. 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-transpror

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

Health

CRAN checks

13OK

Slowest check: 11.8 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

98%

Documentation · exports

28

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
OK2026-06-27
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-21
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 8 earlier snapshots

ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-12
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-05-10
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-30
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-28
12 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 137 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 94%
Documented parameters: 100%
Return-value docs: 100%
References docs: 8%

Downloads

5.5K

CRAN downloads in the past year

Rank #6,691 · ~15/day · ~456/mo

Releases R versions

Daily download trend is not available in this view yet.

32330 days

1.3K90 days

5.5K1 year

Compare downloads with other packages →

Also on138 r2u

Repository

GitHub ↗ sssydysss/transprorbook

5Stars

0Forks

0Open issues

0Open PRs

0Releases

46Commits

1Contributors

data-visualizationtranscriptome-data-analysis

46 commits · Last activity 2024-07-20

Stars over time

2025-02-22 · 52026-07-07 · 5

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/sssydysss/transprorbook on 2026-08-16.

Continuous integration (1)

GitHub Actions

Docs source (1)

Quarto project

Lint, format, editor (2)

VS CodeJetBrains/.idea

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

Dependencies

Declared dependencies

28 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.3.0

Imports (28)

magrittrstatsdplyr rlang tibble sva DESeq2utilsedgeR limma ggplot2 ggVennDiagram ggdensity ggpubr ggtreegridggraph tidygraph tidyr stringr geomtextpath ggnewscale Hmisc circlizegraphicsspiralize ComplexHeatmapgrDevices

LinkingTo (0)

none

Suggests (5)

prettydoc knitr ggtreeExtra rmarkdown systemfonts

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Dongyue Yu

Author, Maintainer, Copyright holder

Authors (1)

Dongyue Yu

Author, Maintainer, Copyright holder

Copyright holders (1)

Dongyue Yu

Author, Maintainer, Copyright holder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.0.7Latest
2025-09-12 · current release · diff ↗
1.0.6
2025-08-26 · diff ↗
1.0.5
2025-06-16 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.3
2025-02-18 · diff ↗
1.0.2
2025-02-15 · diff ↗
unarchivedReturned to CRAN
2025-02-14
archivedRemoved from CRAN
2025-02-02
issues were not corrected in time
0.0.6
2024-12-10
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-12-10
Total releases: 6 / 2 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.3.0
Bundled data: 163 KB / 2 files
Download size: 1.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("TransProR")

Format

Yu, D. (2025). TransProR: Analysis and Visualization of Multi-Omics Data (Version 1.0.7) [Computer software]. https://doi.org/10.32614/CRAN.package.TransProR

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 TransProR version 1.0.7 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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