perturbMatchData

perturbMatchData provides the perturbMatch reference perturbation expression signatures through Bioconductor ExperimentHub.

Installation

BiocManager::install("perturbMatchData")

Access data

library(perturbMatchData)

perturbMatch_reference()

se <- perturbMatch_chrdir()

Data provenance

Raw counts come from the GEO RNA-seq counts matrices for each series, computed against GRCh38.p13. Case and control groups, the perturbed gene and the perturbation type were annotated with the LLM-GeoSig Nextflow pipeline, which also computes the signatures. inst/scripts/run_nextflow.sh records that run. make-data.R assembles the signatures into one HDF5 file of assays and a signature annotation per dataset, and make-metadata.R writes the ExperimentHub metadata.

Data are hosted on Zenodo at https://doi.org/10.5281/zenodo.21792179.