News: Published: GeneSCF: a real-time based functional enrichment tool with support for multiple organisms
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gravatar for EagleEye
14 months ago by
EagleEye4.8k
Sweden
EagleEye4.8k wrote:

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).

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

/EagelEye

ADD COMMENTlink modified 14 months ago by Mike880 • written 14 months ago by EagleEye4.8k
2

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".

ADD REPLYlink written 13 months ago by avalexeyenko20

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

ADD REPLYlink written 13 months ago by EagleEye4.8k

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

ADD REPLYlink written 14 months ago by Mike880

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

ADD REPLYlink modified 14 months ago • written 14 months ago by genomax37k

Sorry for that. Soon will be updated for OSX.

ADD REPLYlink written 14 months ago by EagleEye4.8k
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