# ------------------------------------------------
# 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 "perturbMatch" in publications use:'
type: software
license: GPL-3.0-only
title: 'perturbMatch: Match Transcriptomics Signatures to Single-Gene Perturbation
  References'
version: 0.99.1
doi: 10.64898/2026.08.08.743502
identifiers:
- type: doi
  value: 10.32614/CRAN.package.perturbMatch
abstract: Matches a query transcriptomics signature against a reference database of
  single-gene perturbation signatures, ranking the perturbations whose expression
  response most resembles the query and so nominating the regulators most likely to
  drive the observed change. Query signatures derived from a differential expression
  result are scored using cosine, GSEA and signed-Jaccard similarity metrics. Reference
  databases are supplied as HDF5-backed SummarizedExperiment objects for memory-efficient
  handling of large perturbation collections, and helper functions rank and visualise
  the best-matching regulators.
authors:
- family-names: Soul
  given-names: Jamie
  email: jamie.soul@liverpool.ac.uk
  orcid: https://orcid.org/0000-0003-2255-6459
preferred-citation:
  type: article
  title: Automated generation of a gene perturbation transcriptomic atlas using large
    language models
  authors:
  - family-names: Soul
    given-names: Jamie
    email: jamie.soul@liverpool.ac.uk
    orcid: https://orcid.org/0000-0003-2255-6459
  - family-names: Young
    given-names: David A.
  journal: bioRxiv
  year: '2026'
  doi: 10.64898/2026.08.08.743502
  url: https://doi.org/10.64898/2026.08.08.743502
repository: https://biocstaging.r-universe.dev
repository-code: https://github.com/soulj/perturbMatch
commit: 48a25c74e5947a044ecdcfb0ded10be4173bf0d9
url: https://github.com/soulj/perturbMatch
date-released: '2026-09-02'
contact:
- family-names: Soul
  given-names: Jamie
  email: jamie.soul@liverpool.ac.uk
  orcid: https://orcid.org/0000-0003-2255-6459