Package: PubMatrixR 1.0.1

PubMatrixR: PubMed Pairwise Co-Occurrence Matrix Construction and Visualization

Queries the 'NCBI' (National Center for Biotechnology Information) Entrez 'E-utilities' API to count pairwise co-occurrences between two sets of terms in 'PubMed' or 'PubMed Central'. It returns a matrix-like data frame of publication counts and can export hyperlink-enabled results in CSV or ODS format. The package also provides heatmap helpers for exploratory visualization of overlap patterns. Based on the method described in Becker et al. (2003) "PubMatrix: a tool for multiplex literature mining" <doi:10.1186/1471-2105-4-61>.

Authors:Tyler Laird [aut], Enrique Toledo [aut, cre]

PubMatrixR_1.0.1.tar.gz
PubMatrixR_1.0.1.zip(r-4.7-any)PubMatrixR_1.0.1.zip(r-4.6-any)PubMatrixR_1.0.1.zip(r-4.5-any)
PubMatrixR_1.0.1.tgz(r-4.6-any)PubMatrixR_1.0.1.tgz(r-4.5-any)
PubMatrixR_1.0.1.tar.gz(r-4.7-any)PubMatrixR_1.0.1.tar.gz(r-4.6-any)
PubMatrixR_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PubMatrixR/json (API)

# Install 'PubMatrixR' in R:
install.packages('PubMatrixR', repos = c('https://toledoem.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/toledoem/pubmatrixr-v2/issues

Pkgdown/docs site:https://toledoem.github.io

On CRAN:

Conda:

bibliometric-analysisbibliometric-visualizationbibliometricsdataminingliterature-miningncbi-databasepubmed

5.08 score 1 stars 6 scripts 269 downloads 3 exports 29 dependencies

Last updated from:fddd355d74. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK141
source / vignettesOK254
linux-releaseOK164
macos-releaseOK90
macos-oldrelOK71
windows-develOK70
windows-releaseOK64
windows-oldrelOK73
wasm-releaseOK129

Exports:plot_pubmatrix_heatmapPubMatrixpubmatrix_heatmap

Dependencies:cellrangerclicpp11farvergluegtablelabelinglifecyclemagrittrmintypbapplypheatmappillarpkgconfigR6RColorBrewerreadODSrematchrlangscalesstringitibbletzdbutf8vctrsviridisLitewithrxml2zip

PubMatrixR with Ligand Receptors
Introduction | Running the search | NCBI API Key (Recommended) | Which genes get the most attention | The full matrix | Heatmaps | System Information
Rendered fromWntExample.Rmdusingknitr::rmarkdown

Last update: 2026-08-20
Started: 2026-08-20

PubMatrixR: Literature Co-occurrence Analysis
Introduction | Acknowledgments | NCBI API Key (Recommended) | Preparing Gene Sets | Making the gene lists from MSigDB | Fallback Example Dataset | Literature Analysis | Running PubMatrixR | Results Table | Visualization | Publication Count Bar Plots | Heatmap with Overlap Percentages | Clean Heatmap | Bar Plots for Asymmetric Lists | Summary | System Information
Rendered fromvignette.Rmdusingknitr::rmarkdown

Last update: 2026-08-20
Started: 2025-10-24