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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "PubMatrixR" in publications use:'
type: software
license: MIT
title: 'PubMatrixR: PubMed Pairwise Co-Occurrence Matrix Construction and Visualization'
version: 1.0.0
doi: 10.1186/1471-2105-4-61
identifiers:
- type: doi
  value: 10.32614/CRAN.package.PubMatrixR
abstract: '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" <https://doi.org/10.1186/1471-2105-4-61>.'
authors:
- family-names: Laird
  given-names: Tyler
  email: tylerscottlaird@gmail.com
- family-names: Toledo
  given-names: Enrique
  email: enriquetoledo@gmail.com
  orcid: https://orcid.org/0000-0002-1460-4708
preferred-citation:
  type: article
  title: 'PubMatrix: a tool for multiplex literature mining'
  authors:
  - family-names: Becker
    given-names: K. G.
  - family-names: Hosack
    given-names: D. A.
  - family-names: Dennis
    given-names: G. Jr
  - family-names: Lempicki
    given-names: R. A.
  - family-names: Bright
    given-names: T. J.
  - family-names: Cheadle
    given-names: C.
  - family-names: Engel
    given-names: J.
  journal: BMC Bioinformatics
  year: '2003'
  month: '12'
  volume: '4'
  doi: 10.1186/1471-2105-4-61
  url: https://pmc.ncbi.nlm.nih.gov/articles/PMC317283/
  start: '61'
repository: https://toledoem.r-universe.dev
repository-code: https://github.com/ToledoEM/PubMatrixR-v2
commit: 92acfd4ea438e30ab22e844a2b6ee4bedaed85d1
url: https://github.com/ToledoEM/PubMatrixR-v2
date-released: '2026-06-03'
contact:
- family-names: Toledo
  given-names: Enrique
  email: enriquetoledo@gmail.com
  orcid: https://orcid.org/0000-0002-1460-4708