R Observatory: Metrics for TransProR version 1.0.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TransProR

1.0.7Package record

Analysis and Visualization of Multi-Omics Data

0packages depend

6.7Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Dongyue YuCRAN page ↗GitHub ↗Issues ↗

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. 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 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-27

Show 10 earlier changesHide 10 earlier changes

ERROR12 OK, 1 ERROR2026-06-21
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-12
NOTE12 OK, 1 NOTE2026-05-10
ERROR12 OK, 1 ERROR2026-05-03
OK12 OK2026-04-25
NOTE13 OK, 1 NOTE2026-03-30
ERROR12 OK, 1 NOTE, 1 ERROR2026-03-28
NOTE13 OK, 1 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.7

READMEYes · 137 wordsVignettesYes · 1 · staticNEWSNoCitation fileNo

Help pages: 53 (1 internal)
Examples that run: 94%44 run in a plain check · 3 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 90%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 8%

Vignettes (1)

TransProR

How these are measured

Downloads

6.7K

CRAN downloads in the past year

Rank #3,934 · ~18/day · ~559/mo

Releases R versions

Daily download trend is not available in this view yet.

1.4K30 days

2.3K90 days

6.7K1 year

Compare downloads with other packages →

Also on73 r2u

How downloads are counted

Repository

sssydysss/transprorbook ↗Account: SSSYDYSSS

5Stars

0Forks

0Open issues

0Open PRs

0Releases

46Commits

1Commit identities

data-visualizationtranscriptome-data-analysis

46 commits · Last activity 2024-07-20 · Discussions: 25 posts

Responsiveness

not measured

Stars over time

2025-02-22 · 52026-07-07 · 5

How these are measured

PracticesBeta

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

Checks run against github.com/sssydysss/transprorbook on 2026-10-11.

Continuous integration (1)

GitHub Actions

Docs source (3)

Quarto project

GitHub Pages site last deployed 2024-07-20 · The repository has a site deploy workflow

Lint, format, editor (2)

VS CodeJetBrains/.idea

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

28 external dependencies (excludes base and recommended)

Installing TransProR adds 127 packages (61 with compiled code, 123 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB. 6 more not on CRAN are not measured.

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.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Dongyue Yu

Releases (6)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.0.7Latest
record
2025-09-12 · current release · diff ↗ ·
removed 3 exports
add_new_tile_layer, circos_fruits, highlight_by_node
1.0.6
record
2025-08-26 · diff ↗
1.0.5
record
2025-06-16 · diff ↗ ·
added 2 exports
StatXspline, stat_xspline
R
R 4.5.0 released · 2025-04-11
1.0.3
record
2025-02-18 · diff ↗
1.0.2
record
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
record
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

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 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 TransProR version 1.0.7 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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