LBDiscover

0.1.0

Literature-Based Discovery Tools for Biomedical Research

0packages depend

2.4Kdownloads / year

28.8%test coverage

12/13checks pass

Overview

About

Maintained by Chao LiuFirst published 2025-06-161 releasesCRAN page ↗GitHub ↗

A suite of tools for literature-based discovery in biomedical research. Provides functions for retrieving scientific articles from 'PubMed' and other NCBI databases, extracting biomedical entities (diseases, drugs, genes, etc.), building co-occurrence networks, and applying various discovery models including 'ABC', 'AnC', 'LSI', and 'BITOLA'. The package also includes visualization tools for exploring discovered connections.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("LBDiscover", 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("chaoliu-cl/LBDiscover")

Development version from chaoliu-cl/LBDiscover. 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-lbdiscover

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-LBDiscover

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-LBDiscover

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 2.3 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.18

28.8%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 374 wordsVignettesNopkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 25%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.4K

CRAN downloads in the past year

Rank #20,145 · ~6/day · ~197/mo

Releases R versions

Daily download trend is not available in this view yet.

14930 days

55490 days

2.4K1 year

Compare downloads with other packages →

Also on102 r2u3 autocran

Repository

GitHub ↗ chaoliu-cl/lbdiscover

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2025-10-05

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/chaoliu-cl/lbdiscover on 2026-07-31.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Research and citation (1)

codemeta.json

Show all practices

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (11)

httr xml2 igraphMatrixutilsstatsgrDevicesgraphicstoolsrentrez jsonlite

LinkingTo (0)

none

Suggests (17)

openxlsx SnowballC visNetwork (>= 2.1.0)spacyrparalleldigest irlba knitr rmarkdown base64enc reticulate testthat mockery covr htmltools data.table tibble

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Chao Liu

Author, Maintainer

Authors (1)

Chao Liu

Author, Maintainer

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-06-16
Total releases: 1 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Download size: 553 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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