This folder contains workflows for TRN analyses:
- Gene-set enrichment analysis (GSEA) of a TF's positive and repressed target genes
- (optional) filter TF-gene interactions according to partial correlation: filter_TRNs_by_pcorr.sh
- runGSEA on each TF's positive and repressed target genes: tfTargets_GSEA_loop.sh
- visualize enrichments with a heatmap: visGSEAenrich_heatmaps_comb.m
- Identify "core" TF regulators for a subset of conditions or celltypes in the gene expression dataset (see: Miraldi et al., 2019)
- (optional) filter TF-gene interactions according to partial correlation: filter_TRNs_by_pcorr.sh
- run GSEA to test whether a TF's postive or repressed targets are enriched in condition or celltype gene signatures: tfTargets_GSEA.sh
- visualize "Top N" core TFs for the condition or celltype in a bargraph: th17_coreAnalysis.m
- Visualize TF degree, positive and negative edges, and overlap with TF-gene interactions in the prior: viz_TF_degree.m