Package: perturbMatch 0.99.1

Jamie Soul

perturbMatch: Match Transcriptomics Signatures to Single-Gene Perturbation References

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:Jamie Soul [aut, cre], Versus Arthritis [fnd]

perturbMatch_0.99.1.tar.gz
perturbMatch_0.99.1.zip(r-4.7-any)perturbMatch_0.99.1.zip(r-4.6-any)perturbMatch_0.99.1.zip(r-4.5-any)
perturbMatch_0.99.1.tgz(r-4.6-any)perturbMatch_0.99.1.tgz(r-4.5-any)
perturbMatch_0.99.1.tar.gz(r-4.7-any)perturbMatch_0.99.1.tar.gz(r-4.6-any)
perturbMatch_0.99.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
perturbMatch/json (API)

# Install 'perturbMatch' in R:
install.packages('perturbMatch', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/soulj/perturbmatch/issues

On CRAN:

Conda:

generegulationtranscriptomicstranscriptiongenesetenrichmentgenetargetgeneexpressiondifferentialexpression

3.30 score 4 scripts 15 exports 100 dependencies

Last updated from:48a25c74e5. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE244
linux-develOK337
source / vignettesOK470
linux-releaseOK435
macos-releaseOK416
macos-oldrelOK286
windows-develOK402
windows-releaseOK365
windows-oldrelOK386
wasm-releaseOK184

Exports:backgroundcalcEnrichmentdownRegulatedenrichmentgetReferenceDatabaseplotRegulatorGSEAplotSimilarityplotVolcanoprepareQueryregulatorGSEAregulatorTableshowtopRegulatorsupRegulatedvolcanoPlot

Dependencies:abindAnnotationDbiAnnotationHubaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsbiocmakeBiocManagerBiocParallelBiocVersionBiostringsbitbit64blobcachemclicodetoolscowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdir.expirydplyrExperimentHubfarverfastmapfastmatchfgseafilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2ggrepelgluegtableh5mreadHDF5Arrayhttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslorg.Hs.eg.dbpillarpkgconfigpngpurrrR6rappdirsRColorBrewerRcpprhdf5rhdf5filtersRhdf5librlangRSQLiteS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrsviridisLitewithrXVectoryaml

Matching a differential expression signature to perturbation references using perturbMatch
Installation | Background | Overview | Reference signatures | How it works | Preparing input data | Load reference expression data | Choosing a full reference database | Map the query to the reference | Starting from a table or CSV file | Calculating regulator scores | Checking a known target | Using an explicit gene set | Visualise the results | Inspecting a single reference signature | Where the perturbed gene ranks: target_gene_percentile | Filtering on the target percentile | Functional enrichment of the regulator hits | Scoring methods available | Comparing scoring methods | Interpreting the score, zscore, and overlap columns | Tuning topN | Parallelisation | Verifying hits before interpretation | Saving results to a file | Related packages | Citation | Session information | Acknowledgements
Rendered fromperturbMatch.Rmdusingknitr::rmarkdown

Last update: 2026-09-02
Started: 2026-08-07

Matching a single-cell RNA-seq response to perturbation references using perturbMatch
Overview | Load the data | Select a cell population | Aggregate into pseudobulk samples | Differential expression | Score candidate regulators | Filtering hits that cannot be human regulators | Visualise the results | Cell-level scoring with singscore | Session information
Rendered fromperturbMatch_singlecell_vignette.Rmdusingknitr::rmarkdown

Last update: 2026-08-07
Started: 2026-08-07

Readme and manuals

Help Manual

Help pageTopics
Background genes from a PerturbMatch objectbackground background,PerturbMatch-method
Calculate enrichmentcalcEnrichment calcEnrichment,SummarizedExperiment-method
Down-regulated genes from a PerturbMatch objectdownRegulated downRegulated,PerturbMatch-method
Enrichment scores from a PerturbMatch objectenrichment enrichment,PerturbMatch-method
Load the perturbMatch reference databasegetReferenceDatabase
PerturbMatch enrichment resultsPerturbMatch-class
Dot plot of regulator GO enrichmentplotRegulatorGSEA
Plot signature similarity scoresplotSimilarity plotSimilarity,PerturbMatch-method
Volcano Plot from a SummarizedExperiment ObjectplotVolcano
Prepare a differential expression result for calcEnrichmentprepareQuery
GO enrichment of perturbMatch regulator hits by GSEAregulatorGSEA
Tidy table of regulator scores from a PerturbMatch objectregulatorTable regulatorTable,PerturbMatch-method
Show a PerturbMatch objectshow,PerturbMatch-method
Top-scoring regulator signaturestopRegulators topRegulators,PerturbMatch-method
Up-regulated genes from a PerturbMatch objectupRegulated upRegulated,PerturbMatch-method
Volcano Plot of Differential Expression ResultsvolcanoPlot