<% _.each(terms.slice(0, 3), function(term, idx) { %>

<%= term._highlightResult.name.value %>

<% }) %>
Tools
Discover the best online tools to assist you in research

GeneSCF

noun_15445_cc Created with Sketch.
 by Santhilal Subhash

Description

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.

Advantages
-----------------------------------------------
- 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.

Discussion

Ask a question or post a review

Santhilal Subhash
PhD student at University of Gothenburg
View profile

Santhilal Subhash

PhD student at University of Gothenburg

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: 2 years ago
Santhilal Subhash
PhD student at University of Gothenburg
View profile

Santhilal Subhash

PhD student at University of Gothenburg

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.

https://www.biostars.org/p/108669/

upvotecomment_icon_normal 5 upvotes 2 comments Reply
Posted: 2 years ago