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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>.
| Version: |
1.0.0 |
| Depends: |
R (≥ 4.1.0) |
| Imports: |
pbapply, pheatmap, readODS, xml2 |
| Suggests: |
dplyr, ggplot2, kableExtra, knitr, rmarkdown, testthat (≥
3.0.0) |
| Published: |
2026-03-12 |
| DOI: |
10.32614/CRAN.package.PubMatrixR (may not be active yet) |
| Author: |
Tyler Laird [aut],
Enrique Toledo 
[aut, cre] |
| Maintainer: |
Enrique Toledo <enriquetoledo at gmail.com> |
| BugReports: |
https://github.com/ToledoEM/PubMatrixR-v2/issues |
| License: |
MIT + file LICENSE |
| URL: |
https://github.com/ToledoEM/PubMatrixR-v2 |
| NeedsCompilation: |
no |
| Citation: |
PubMatrixR citation info |
| Materials: |
README, NEWS |
| CRAN checks: |
PubMatrixR results |
Documentation:
Downloads:
Linking:
Please use the canonical form
https://CRAN.R-project.org/package=PubMatrixR
to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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