{Gene Set Clustering based on Functional annotation}

GeneSCF serves as command line tool for clustering the list of genes given by the users based on functional annotation (Geneontology, KEGG, REACTOME and NCG). It requires gene list in the form of Entrez Gene ID (UIDs) or Official gene symbols as a input.

The advantage of using GeneSCF over other enrichment tools is that, it performs enrichment analysis in real-time (v1.1 and above) by accessing source databases.

Available Versions

FeaturesGeneSCF v1.0GeneSCF v1.1
Entrez GeneID (input support)
Gene Symbols (input support)
Multiple database support
Multi-organism support X
Real-time analysis X
Graphical output X
User-defined database support X
Ensembl ID (input support) X X

System requirements

GeneSCF only works on Linux system, it has been successfully tested on Ubuntu, Mint and Cent OS. Other distributions of Linux might work as well. If something goes wrong, please test whether these commands are woking fine on your teminal, awk, cat, gzip, wget, rm, mkdir, sort, date, sed, paste, join, grep, curl, echo

Report issues regarding GeneSCF on github and follow more discussions on biostars