Quick Start

A 60-second tour of both the GUI and the CLI.

GUI in 5 clicks

cis-gs-gui

  1. Step 1 — Promoters: drop a FASTA + GFF3, set promoter length, click Extract.

  2. Step 2 — Motif Search: click Import from PlantTFDB, pick your species, tick motifs, Import Selected → Step 2.

  3. Step 2 (still): click Scan — hits CSV with hypergeometric p-values appears.

  4. Step 7 — KEGG Enrichment: select a KEGG organism from the live dropdown, paste your gene list, Run.

  5. Done — CSVs and SVGs land in ~/CisGS-Workspace/.

CLI wizard

cis-gs wizard

The wizard auto-detects what you already produced and offers the next sensible step. Arrow keys to navigate, Enter to confirm.

One-liner CLI examples

Extract 2 kb promoters:

cis-gs extract --fasta genome.fa --gff annot.gff3 \
               --upstream 2000 --out promoters.fa

Scan with a MEME motif file:

cis-gs search --promoters promoters.fa --motifs motifs.meme \
              --out hits.csv

Convert NCBI Gene IDs → Ensembl in one batched request:

cis-gs id-convert --species human --target ensembl \
                  --infile genes.txt --out ensembl.csv

KEGG enrichment on the top module:

cis-gs enrich-kegg --organism ath --genes top_module.txt \
                   --out kegg.csv

Every command supports -i / --interactive to be walked through it.