Command Reference

cis-gs fetch

cis-gs fetch --organism "Arabidopsis thaliana" --out ./refs/

Searches NCBI Assembly, picks the latest RefSeq, downloads FASTA + GFF3.

cis-gs extract

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

cis-gs search

cis-gs search --promoters promoters.fa --motifs motifs.meme \
              [--allow-overlap] [--rc] --out hits.csv

cis-gs feed

cis-gs feed --hits hits.csv --expression expr.csv \
            [--mapping mapping.csv] [--gff3 annot.gff3] \
            --out matched.csv

cis-gs coexpr

cis-gs coexpr --expression expr.csv \
              [--method pearson|spearman] \
              [--soft-power 6] \
              [--module-method louvain|hierarchical] \
              --out network.gexf

cis-gs kmeans

cis-gs kmeans --expression expr.csv -k 6 \
              [--seed 42] [--elbow] --out clusters/

cis-gs enrich-kegg

cis-gs enrich-kegg --organism ath --genes top_module.txt \
                   [--background bg.txt] \
                   [--min-overlap 2] [--min-set-size 5] \
                   --out kegg.csv

cis-gs id-convert

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

Routes through MyGene.info via a batched POST (chunks of 1 000 IDs) with a live progress bar. ~60× faster than the legacy per-ID GET.