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", 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.

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

Health

CRAN checks

1ERROR12OK

Failing flavors

ERROR r-oldrel-macos-arm64

Slowest check: 5.2 min · r-devel-linux-x86_64-fedora-clang

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

Documentation

Documentation signals are not tracked yet for this package.

Downloads

3.8K

CRAN downloads in the past year

Rank #8,387 · ~10/day · ~315/mo

DeSciDe Releases R versions

Daily download trend is not available in this view yet.

29430 days

1.3K90 days

3.8K1 year

Compare downloads with other packages →

Also on127 r2u

Repository

GitHub ↗ camdouglas/descide

1Stars

0Forks

0Open issues

0Open PRs

0Releases

66Commits

1Contributors

66 commits · Last activity 2026-04-09

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/camdouglas/descide on 2026-07-19.

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

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

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Cameron Douglas

Author, Maintainer

Authors (1)

Cameron Douglas

Author, Maintainer

Package Timeline

4 releases. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.3Latest
2026-04-09 · current release · diff ↗
1.0.2
2025-08-31 · diff ↗
1.0.1
2025-06-20 · diff ↗
1.0.0
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
Download size: 1.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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