This repository contains scripts, data, and tutorials to accompany the SalmonAct resource, a regulon tailored for inferring transcription factor activities in Salmonella. SalmonAct is a signed and directed prior knowledge network (PKN) made for Salmonella transcriptomics, expanding on the SalmoNet2 interaction resource. Developed for compatibility with decoupleR, an R and Python library, this repository enables transcription factor activity estimation, aiding researchers in exploring Salmonella biology.
SalmonAct PKN: A curated network of signed and directed interactions involving 191 transcription factors for Salmonella. Accessible in the data/db/ folder, named salmonact.tsv.
Data Compatibility: Harmonized interaction data from databases like PRODORIC, CollecTF, RegPrecise, SalComRegulon and RegulonDB, formatted for decoupleR.
Analysis Scripts: R scripts to replicate differential expression and transcription factor activity analyses shown in the manuscript.
Mapping Table: ID mapping table based on protein orthology established for SalmoNet2 to aid analysis in 20 strains
For a detailed tutorial please navigate to the tutorial folder, or follow the steps replicating the analysis shared in the manuscript in scripts/salmonact_notebook.Rmd.