The 7-Step Workflow

Cis-GS organises every analysis into seven numbered steps that mirror the tabs in the GUI. Each step writes to ~/CisGS-Workspace/ so you can pause, swap tools, and resume.

#	Step	What it does	Key output
1	Promoters	Strand-aware promoter extraction from FASTA + GFF3	promoters.fa
2	Motif Search	IUPAC / MEME / PlantTFDB / AnimalTFDB scanning with hypergeom p-vals	hits.csv
3	Motif Logos	logomaker sequence logos with IC shading	per-motif SVG / PNG
4	Expression Feeding	Joins hits with an expression CSV via 3 ID-mapping methods	expression_matched.csv
5	Coexpression	Pearson / Spearman / WGCNA soft-threshold, Louvain modules	network.gexf
6	K-means	Elbow + silhouette, deterministic seeding	clusters/*.txt
7	KEGG Enrichment	Live REST query, hypergeom ORA, BH-FDR	kegg_enrichment.csv

Each step is independent — you can start at any point if you already have the inputs that step expects.