DeSciDe

1.0.3

Tool for Unbiased Literature Searching and Gene List Curation

0packages depend

3.8Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Cameron DouglasFirst published 2025-04-294 releasesCRAN page ↗GitHub ↗

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")

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

pak::pak("camdouglas/DeSciDe")

Development version from camdouglas/DeSciDe. Requires the pak package.

Release

# one-time r2u setup for Ubuntu (noble)

curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash

# then install

sudo apt install r-cran-descide

Fast Ubuntu binaries via r2u (no compilation). Run the setup once per machine.

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

Health

CRAN checks

1ERROR12OK

Failing flavors

ERROR r-oldrel-macos-arm64

Code health

Yes

Tests · ratio 0.37

not tracked

Coverage

100%

Documentation · exports

Yes

Vignettes

Yes

README

Dependencies · direct

Check history

ERROR2026-03-21
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

3.8K

CRAN downloads in the past year

Rank #8,001 · ~10/day · ~316/mo

47030 days

1.4K90 days

3.8K1 year

Also on127 r2u

Source & community

GitHub ↗

Repository stars, issues, and contributor activity are not tracked yet.

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

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

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code

1,650Lines of code

10Exported functions

Code & tests

Open call graph →

Line coverage

–

Expression

–

Tests / Examples

–

Functions

10 10 exported

Complexity

5.9 avg / 13 max

Call network

10 nodes / 9 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (1)

Maintainer (1)

Cameron Douglas iD

Author, Maintainer

Release timeline

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

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

Package metadata

First published: 2025-04-29
Total releases: 4 / 1 yrs
License: MIT + file LICENSE OSI
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet