PubMed Pairwise Co-Occurrence Matrix Construction and Visualization R package PubMatrixR version 1.0.0 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>. Software Depends: R (>= 4.1.0) Imports: pbapply, pheatmap, readODS, xml2 Suggests: dplyr, ggplot2, kableExtra, knitr, rmarkdown, testthat (>= 3.0.0) Enrique Toledo <enriquetoledo@gmail.com> Comprehensive R Archive Network (CRAN) Tyler Laird [aut], Enrique Toledo [aut, cre] (ORCID: <https://orcid.org/0000-0002-1460-4708>) MIT + file LICENSE (https://CRAN.R-project.org/package=PubMatrixR/LICENSE) 2026-03-12 application/tgz https://CRAN.R-project.org/package=PubMatrixR doi:10.32614/CRAN.package.PubMatrixR