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GeneSCF specifications
Information
| Unique identifier | OMICS_10275 |
|---|---|
| Name | GeneSCF |
| Alternative name | Gene Set Clustering based on Functional annotation |
| Software type | Package/Module |
| Interface | Command line interface |
| Restrictions to use | Academic or non-commercial use |
| Input data | The standard input for GeneSCF is plain text document (text/plain) containing a list of genes in the form of official gene symbols. |
| Output data | The final output from GeneSCF is a table (text/tab-separated file, TSV) with list of ranked functions based on the number of hits from the user provided gene list. It also contains column with probability value (P-value) obtained by Fisher’s exact test using the contingency table and also columns containing false discovery rate (FDR) values using different multiple hypothesis correction methods. |
| Operating system | Unix/Linux |
| Programming languages | Perl, Shell (Bash) |
| License | GNU General Public License version 3.0 |
| Computer skills | Advanced |
| Version | 1.1 |
| Stability | Stable |
| Requirements |
R, ggplot
|
| Maintained | Yes |
Taxon
-
Primates
- Homo sapiens
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Versioning
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Documentation
- Documentation: http://genescf.kandurilab.org/documentation.php
Maintainer
- person_outline Chandrasekhar Kanduri <>
Open Desktop
GeneSCF successful on Windows 10 bash (version 1607)
#3 opened on 2017-02-10 by Santhilal Subhash • 0 answers
2017-02-10, 14:54
--------------------- 09/02/2017 --------------------------- GeneSCF v1.1 (patch release 2) News : All features are successfully tested on Microsoft Windows 10 bash (version 1607) - require installation of 'unzip' utility on windows bash using 'sudo apt-get install unzip'
Open Desktop
GeneSCF for multiple organisms
#2 opened on 2017-01-25 by Santhilal Subhash • 0 answers
2017-01-25, 18:12
New version of GeneSCF is designed to handle information from more than 4000 organisms from freely available prominent functional databases like KEGG, Reactome and Gene Ontology.
Open Desktop
GeneSCF: Advice to users
#1 opened on 2017-01-14 by Santhilal Subhash • 0 answers
2017-01-14, 09:44
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/
Publications for Gene Set Clustering based on Functional annotation
GeneSCF: a real-time based functional enrichment tool with support for multiple organisms.
MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA-DNA triplex structures.
GeneSCF in pipeline
PAN cancer analysis of S phase enriched lncRNAs identifies oncogenic drivers and biomarkers
[…] the significant candidates were filtered with log-fold change > ± 1 and fdr ≤ 0.05., the significantly deregulated genes from sirna knockdown samples were tested for pathway enrichment using tool genescf v1.1. the parameters for genescf were set to database reactome with background genes 20,345 (all protein-coding genes from gencode v19 annotation used in this study). the enriched functions […]
GeneSCF in publications
(2)PAN cancer analysis of S phase enriched lncRNAs identifies oncogenic drivers and biomarkers
[…] using the serum starvation method (supplementary fig. ).fig. 1, since lncrnas exert their actions via regulating protein-coding rnas in cis and/or trans–, we performed enrichment analysis using genescf for the neighboring protein-coding genes (within ±50 kb window of s-phase-specific lncrnas). interestingly, the neighboring protein-coding genes associated with etu-labeled s-phase-specific […]
[…] repeat elements obtained.fig. 2 , the pathway enrichment analysis and cancer enrichment analysis on clldmgs was carried out with the help of a command line functional enrichment tool called genescf v1.1 (gene set clustering based on functional annotation) [, ]. we used genescf with parameters, two different database kegg pathways and ncg (network of cancer genes 4.0) [], ensembl […]
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