orthosData

orthosData is an R/ExperimentHub package providing access to data objects required for the methods implemented in the orthos package for mechanistic studies using differential gene expression experiments.

It currently encompasses data for over 100,000 differential gene expression mouse and human experiments distilled and compiled from the ARCHS4 database* as well as associated pre-trained variational models.

Together with orthos it was developed  to provide a better understanding of the effects of experimental treatments on gene expression and to help map treatments to mechanisms of action.

All orthosData datasets are publicly available through Zenodo, doi:10.5281/zenodo.7554914 according to open data standards and licenses under the Creative Commons Attribution 4.0 International license (CC-BY 4.0).

* Lachmann A, Torre D, Keenan AB, Jagodnik KM, Lee HJ, Wang L, Silverstein MC, Ma’ayan A. Massive mining of publicly available RNA-seq data from human and mouse. Nature Communications 9. Article number: 1366 (2018), doi:10.1038/s41467-018-03751-6