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# CITATION.cff 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 "IsoNetAnalyzeR" in publications use:'
type: software
license: MIT
title: 'IsoNetAnalyzeR: Isoform-Level Protein Interaction Network Analysis'
version: 0.99.0
abstract: Compares predicted protein-interaction neighbourhoods of transcript isoforms.
  The user supplies isoform seeds labelled "up" or "down", for example the isoforms
  that gain or lose usage in a differential transcript usage analysis. Each seed set
  is expanded in a bundled isoform-resolved predicted interaction network, or in a
  user-supplied igraph network, and the resulting neighbourhoods are compared per
  gene and summarised across genes. The package also provides connected-component
  analysis, network diagnostics, plots, and over-representation and gene set enrichment
  analysis of neighbourhood statistics. Protein-identical transcripts are resolved
  to shared representatives, and annotated nonsense-mediated and non-stop decay transcripts
  are excluded by default. Statistical testing of isoform usage remains upstream of
  the package.
authors:
- family-names: Kanakoglou
  given-names: Dimitrios S.
  email: dimkan@dtu.dk
  orcid: https://orcid.org/0000-0001-7735-2029
- family-names: Mumm
  given-names: Nikolas A.
  email: s242825@dtu.dk
  orcid: https://orcid.org/0009-0009-5751-0291
repository: https://biocstaging.r-universe.dev
repository-code: https://github.com/IsoformAnalysisGroup/IsoNetAnalyzeR
commit: 7197e6ff5d117f3c95792d104917eab67842aeb9
url: https://github.com/IsoformAnalysisGroup/IsoNetAnalyzeR
date-released: '2026-11-03'
contact:
- family-names: Kanakoglou
  given-names: Dimitrios S.
  email: dimkan@dtu.dk
  orcid: https://orcid.org/0000-0001-7735-2029