{Gene Set Clustering based on Functional annotation}

GeneSCF Source (All versions)

GeneSCF v1.1-p2 (patch release 2)	Download (linux)	2017/01/13 2017/07/07* 2019/05/19*	4.4M	6196 downloads
GeneSCF v1.1-p1 (patch release 1)	Discontinued (01/Jan/2017)	2016/07/24	4.6M	364 downloads
GeneSCF v1.1	Discontinued (01/Jan/2017)	2016/01/28	4.7M	374 downloads
GeneSCF v1.0	Download (linux)	2015/06/05	2.9M	2846 downloads

*: minor change in code.

Database Information

Following information in table is updated on 2017/07/07.

Database	Pathways/process Entries	Gene Entries
KEGG	320	gi:7,282
Reactome	1,960	gs:10,772/gi:10,563
Gene Ontology (BP)	11,720	gs:17,431/gi:17,127
Gene Ontology (MF)	4,090	gs:17,399/gi:17,114
Gene Ontology (CC)	1,613	gs:18,586/gi:18,240

GeneSCF Major Releases

Features GeneSCF v1.0 GeneSCF v1.1

Release 2013-2015 2016

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

Features	GeneSCF v1.0	GeneSCF v1.1
Release	2013-2015	2016
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

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Change Logs and Updates

2019/05/19: GeneSCF v1.1 changes

- Due to changes in HTTP's request and response code, GeneSCF has to undergo some minor changes in some of the modules. Downloading updated version solves issues related to database retrieval (prepare_database module).
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2017/07/07: GeneSCF v1.1 changes

- Sorry for the inconvenience. Due to changes in KEGG API (Release 83.0, July 1, 2017), GeneSCF database modules was updated to work with recent database releases.
- Default databases updated to current versions for Human (hsa/goa_human/Hs), KEGG, Gene Ontology (GO) and Reactome on 2017/07/07.

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2017/06/01 [14:15 (CEST)]: Corrected gene id conversion issues (from gene symbols to gene ids) for organisms other than human while performing enrichment analysis with KEGG (not affected for those who used prepare_database module)

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2017/02/09: GeneSCF v1.1 (patch release 2) News - All features are successfully tested on Windows 10 bash (version 1607)

Note: Require installation of 'unzip' utility on windows bash using 'sudo apt-get install unzip'
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2017/01/13: GeneSCF v1.1 (patch release 2) Fixes - Release notes

- Due to changes (January 2017 release) in source databases KEGG and Gene Ontology, GeneSCF database modules has to be updated to work with recent database releases.

List of solved issues:

1) Empty output files
2) KEGG not working with GeneSymbols
3) Some organisms from Gene Ontology giving errors or not able to process

Contributions:

Yohann Lelievre (Task: Reporting issue)
Solenne Dumont (Task: Reporting issue)
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