Package: perturbMatchData
Title: Reference Perturbation Signatures from GEO RNA-seq Experiments
Version: 0.99.0
Authors@R: c(
    person(
        "Jamie", "Soul",
        email = "jamie.soul@liverpool.ac.uk",
        role = c("aut", "cre"),
        comment = c(ORCID = "0000-0003-2255-6459")
    ),
    person("Versus Arthritis", role = "fnd")
    )
Description: Provides the reference perturbation expression signatures
        used by the perturbMatch package, which ranks the single-gene
        perturbations whose expression response most resembles a query
        signature. Each reference signature summarises the differential
        expression observed after a single-gene perturbation
        (knockdown, knockout or overexpression) in a human RNA-seq
        experiment deposited in the Gene Expression Omnibus. Signatures
        are summarised either by the characteristic direction method or
        by limma, each with and without surrogate variable analysis
        batch correction, giving four datasets served as HDF5-backed
        SummarizedExperiment objects.
License: MIT + file LICENSE
URL: https://github.com/soulj/perturbMatchData
BugReports: https://github.com/soulj/perturbMatchData/issues
Encoding: UTF-8
biocViews: ExperimentHub, ExperimentData, ExpressionData, RNASeqData,
        SequencingData, Homo_sapiens_Data, GEO
Depends: R (>= 4.5.0)
Imports: ExperimentHub, HDF5Array, S4Vectors, SummarizedExperiment
Suggests: BiocStyle, curl, knitr, rmarkdown, testthat
VignetteBuilder: knitr
Config/testthat/edition: 3
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Config/pak/sysreqs: libicu-dev libpng-dev libssl-dev zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-08-07 10:43:02 UTC
RemoteUrl: https://github.com/BiocStaging/perturbMatchData
RemoteRef: HEAD
RemoteSha: 02b61aa9c7638cccb73e3ddef512635f7e382f3f
NeedsCompilation: no
Packaged: 2026-09-21 11:34:54 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>
