News:Published: GeneSCF: a real-time based functional enrichment tool with support for multiple organisms

Question

[EagleEye]

We are happy to announce that, GeneSCF is now published in BMC bioinformatics. We would like to thank everyone for their support and encouragement. We will be constantly working on improving GeneSCF to include exciting features in future (coming soon).

• Complete documentation on biostar
• Discussions on biostar for past two years
• Project webpage
• Report issues on GitHub, Biostars and email ([e-mail])

Abstract

Background

High-throughput technologies such as ChIP-sequencing, RNA-sequencing, DNA sequencing and quantitative metabolomics generate a huge volume of data. Researchers often rely on functional enrichment tools to interpret the biological significance of the affected genes from these high-throughput studies. However, currently available functional enrichment tools need to be updated frequently to adapt to new entries from the functional database repositories. Hence there is a need for a simplified tool that can perform functional enrichment analysis by using updated information directly from the source databases such as KEGG, Reactome or Gene Ontology etc...[+]more

/EagleEye

[avalexeyenko]

Are you aware that your counts for 2x2 table are wrong? The last two terms should be:

n12 | k - x

n22 | N - [ k + d ] + x so that n11 + n12 + n21 + n22 sum up to all genes from the genome. That is why the table is called "contingency table".

[EagleEye]

Hi avalexeyenko,

First of all thanks for your interest and pointing out the mistakes in the article. We are sorry for the typographical error in the text. As you said we mistakenly used 'n12 | k' in the place of 'n12 | k - x' and also 'n22 | N - [ k + d ]' in the place of 'n22 | N - [ k + d ] + x'.

We will correct this mistake in the published article by providing 'erratum'. We wait for some more weeks for people to find mistakes in the manuscript. Also please let us know, if you find other mistakes in the article.

Thanks,

/Santhilal

[Mike]

Its only works on Linux environment, still not for OSX operating environment.

[GenoMax]

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

[EagleEye]

Sorry for that. Soon will be updated for OSX.