Package: perturbMatch
Type: Package
Title: Match Transcriptomics Signatures to Single-Gene Perturbation
        References
Version: 0.99.1
Authors@R: c(
    person("Jamie", "Soul", role = c("aut", "cre"), email = "jamie.soul@liverpool.ac.uk", 
           comment = c(ORCID = "0000-0003-2255-6459")),
    person("Versus Arthritis", role = "fnd")
  )
Description: 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.
Depends: R (>= 4.5.0)
Imports: methods, AnnotationDbi, org.Hs.eg.db, SummarizedExperiment,
        BiocFileCache, BiocParallel, ExperimentHub, dplyr, ggplot2,
        HDF5Array, fgsea, DelayedMatrixStats, DelayedArray,
        MatrixGenerics, S4Vectors, cowplot, ggrepel, rlang
License: GPL-3
URL: https://github.com/soulj/perturbMatch
BugReports: https://github.com/soulj/perturbMatch/issues
biocViews: GeneRegulation, Transcriptomics, Transcription,
        GeneSetEnrichment, GeneTarget, GeneExpression,
        DifferentialExpression
VignetteBuilder: knitr
RoxygenNote: 7.3.2
Encoding: UTF-8
Suggests: testthat, curl, rmarkdown, BiocStyle, knitr, GO.db, airway,
        DESeq2, muscData, scuttle, SingleCellExperiment, singscore,
        scater, scales, tibble
Collate: 'perturbMatch-package.R' 'perturbMatch_class.R'
        'perturbMatch_get_reference_database.R'
        'perturbMatch_prepareQuery.R' 'perturbMatch_calcEnrichment.R'
        'method_cosine.R' 'method_gsea.R' 'method_jaccard.R'
        'perturbMatch_plot_similarity.R' 'perturbMatch_regulator_go.R'
        'perturbMatch_volcanoPlot.R'
Config/pak/sysreqs: libicu-dev libpng-dev libssl-dev zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-09-02 15:40:29 UTC
RemoteUrl: https://github.com/BiocStaging/perturbMatch
RemoteRef: HEAD
RemoteSha: 48a25c74e5947a044ecdcfb0ded10be4173bf0d9
NeedsCompilation: no
Packaged: 2026-10-13 13:47:39 UTC; root
Author: Jamie Soul [aut, cre] (ORCID: <https://orcid.org/0000-0003-2255-6459>),
  Versus Arthritis [fnd]
Maintainer: Jamie Soul <jamie.soul@liverpool.ac.uk>