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 by Santhilal Subhash


Gene Set Clustering based on Functional annotation (GeneSCF)
GeneSCF is more reliable compared to other functional enrichment tools because of its ability to use reference functional databases in real-time to perform enrichment analysis. It is an easy-to-integrate tool with other pipelines available for downstream analysis of high-throughput data. Since the tool is designed to be ready-to-use, there is no need for any complex compilation and installation procedures.

- Real-time functional enrichment analysis, do not have to depend on tools to get updated.
- Easy for computational biologists to integrate this simple tool with their NGS pipeline.
- GeneSCF supports more organisms.
- Enrichment analysis for Multiple gene list using Multiple source database (GO,KEGG, REACTOME and NCG) in single run.
- Download complete GO terms/Pathways/Functions with associated genes as simple table format as a plain text file.


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Santhilal Subhash
Post-doc at Karolinska Institute
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Santhilal Subhash

Post-doc at Karolinska Institute

GeneSCF successful on Windows 10 bash (version 1607) Oval 17

--------------------- 09/02/2017 ---------------------------

GeneSCF v1.1 (patch release 2) News : All features are successfully tested on Microsoft Windows 10 bash (version 1607)

Note: require installation of 'unzip' utility on windows bash using 'sudo apt-get install unzip'

upvotecomment_icon_normal 6 upvotes 0 comments Reply
Posted: 4 years ago
Santhilal Subhash
Post-doc at Karolinska Institute
View profile

Santhilal Subhash

Post-doc at Karolinska Institute

GeneSCF : Advice to users Oval 17

Due to recent changes (naming convention in FTP files) from the database KEGG (01/January/2017) and Gene Ontology (January 2017), the GeneSCF (v1.1 and v1.1-p1) file retrieval utility was unsuccessful with following issues when using update mode (--mode=update),

Example of reported issue: https://www.biostars.org/p/231071/

Other possible issues:
- Creating empty output files

- Less number of genes mapping to KEGG when using GeneSymbol as input

- Some organism from Gene Ontology was not supported

The above mentioned issues was faced by GeneSCF v1.1, v1.1-p1 users from 01/January/2017. All the problems are now rectified with new patch release GeneSCF v1.1-p2 (13/January/2017).

Download: http://genescf.kandurilab.org/downloads.php

Thanks to all users for supporting GeneSCF and please report if there is any problem. We will continue to work on GeneSCF improvements by considering users feedback.


upvotecomment_icon_normal 5 upvotes 2 comments Reply
Posted: 4 years ago