R Observatory: Metrics for DeSciDe version 1.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

DeSciDe

1.0.3Package record

Tool for Unbiased Literature Searching and Gene List Curation

0packages depend

3.9Kdownloads / year

–test coverage

12/13flavors OK

Overview

About

Maintained by Cameron DouglasCRAN page ↗GitHub ↗Issues ↗

Designed for genomic and proteomic data analysis, enabling unbiased PubMed searching, protein interaction network visualization, and comprehensive data summarization. This package aims to help users identify novel targets within their data sets based on protein network interactions and publication precedence of target's association with research context based on literature precedence. Methods in this package are described in detail in: Douglas et al. (2025) doi:10.1039/D5MO00160A. Key functionalities of this package also leverage methodologies from previous works, such as: - Szklarczyk et al. (2023) doi:10.1093/nar/gkac1000 - Winter (2017) doi:10.32614/RJ-2017-066.

Install

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

install.packages("DeSciDe", 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("camdouglas/DeSciDe")

Development version from camdouglas/DeSciDe. 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-descide

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

1ERROR12OK

Check messages

ERRORpackage dependenciesr-oldrel-macos-arm64

Package required but not available: ‘STRINGdb’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

CRAN check page ↗

Slowest check: 4.2 min · r-oldrel-windows-x86_64

Status changes

ERROR12 OK, 1 ERRORNow
ERROR13 OK, 1 ERROR2026-03-21
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.3

READMEYes · 407 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Description cites an R Journal article

Help pages: 10
Examples that run: 70%7 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran) · 2 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

DeSciDe Vignette HTML

How these are measured

Downloads

3.9K

CRAN downloads in the past year

Rank #10,025 · ~11/day · ~324/mo

Releases R versions

Daily download trend is not available in this view yet.

39830 days

99290 days

3.9K1 year

Compare downloads with other packages →

Also on86 r2u

How downloads are counted

Repository

camdouglas/descide ↗Account: camdouglas

1Stars

0Forks

0Open issues

0Open PRs

0Releases

66Commits

1Commit identities

66 commits · Last activity 2026-04-08

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-05-08 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/camdouglas/descide on 2026-10-11.

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Installing DeSciDe adds 48 packages (29 with compiled code, 52 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB. 2 more not on CRAN are not measured.

Depends (1)

R >= 4.0.0

Imports (13)

rentrez ComplexHeatmap circlize STRINGdb data.table igraph ggplot2 openxlsx dplyr tidyr magrittr tibble ggrepel

LinkingTo (0)

none

Suggests (4)

testthat knitr rmarkdown withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (1)

Cameron Douglas

Author, Maintainer since 1.0.0 (2025)

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.0.3Latest
record
2026-04-09 · current release · diff ↗
1.0.2
record
2025-08-31 · diff ↗
1.0.1
record
2025-06-20 · diff ↗
1.0.0
record
2025-04-29
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-04-29
Total releases: 4 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0.0
Download size: 1.4 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("DeSciDe")

Format

Douglas, C. (2026). DeSciDe: Tool for Unbiased Literature Searching and Gene List Curation (Version 1.0.3) [Computer software]. https://doi.org/10.32614/CRAN.package.DeSciDe

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 DeSciDe version 1.0.3 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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