The most popular Alternative to David?

Question

[bxia]

David is down currently?

I wonder what is the most popular alternative to David..(unfornately I only know David..)

Thanks

[GenoMax]

Gene Set Clustering based on Functional annotation (GeneSCF) and GeneSCF (Gene Enrichment Tool): Advice to users

[bxia]

Does it support zebro fish?

[GenoMax]

Yes it does: C: Gene Set Clustering based on Functional annotation (GeneSCF)

[bxia]

I tried it, it throw me an error as "Error opening in database file at /home/tmhbxx3/tools/GeneSCF/class/functional_class3.pl line 97."

Any idea?

Thanks

[GenoMax]

EagleEye participates here regularly and should be along to help.

[bxia]

Thanks, looks like the original download of geneSCF doesn't include any db except from human.

[EagleEye]

Hello, the initial release was only for Human database. The new/recent versions v1.1 and above supports more number of organisms (default download comes with human/Homo sapiens). If you have multiple organisms and multiple list, GeneSCF is perfect for you.

For the error, please post the commandline you used to run GeneSCF.

Example command:

One step: Update mode (database download + enrichment analysis):

./geneSCF -m=update -i=INPUTgene.list -t=gid -db=KEGG -o=/ExistingOUTPUTfolder/ -org=dre --plot=yes --background=15000

If one-step throws some error try Two-step process below.

Two-step

./prepare_database -db=KEGG -org=dre **(Downloading database)**

./geneSCF -m=normal -i=INPUTgene.list -t=gid -db=KEGG -o=/ExistingOUTPUTfolder/ -org=dre --plot=yes --background=15000 **(Enrichment analysis)**

System Requirement for GeneSCF: GeneSCF only works on Linux system, it has been successfully tested on Ubuntu, Mint and Cent OS. Other distributions of Linux might work as well.

Check FAQs for the rectified errors & GitHub issues page

[bxia]

Hi, I use 'update' to update the db.

Here is the error message:

Illegal division by zero at /GeneSCF/class/lib/List/Vectorize/lib/List.pl line 599, <IN2> chunk 1.
Tue Jan 31 10:50:58 CST 2017 finished processing

Here is my command:
/geneSCF -m=update -i=up.txt -t=sym -db=KEGG -o=./ -p=no -org=mmu -bg=22322

Thanks

[EagleEye]

As I mentioned in my previous reply, try two-step process. Also try to provide complete path for input-file and output-folder. Please let me know, if there is still problem.

[WouterDeCoster]

If that's a requirement it would have been better to put that in your initial question...

[bxia]

it is not. I have multiple data from different organisms, just realized one is from zebrafish.. I know David 6.8 could do zebrafish, so that is the question come from.

[Sej Modha]

KEGG Pathway analysis tool

[RossCampbell]

I like the Gene Ontology Consortium

[Malcolm.Cook]

but, but, DAVID is up: https://david.ncifcrf.gov/

Answer 1

[WouterDeCoster]

I really like Enrichr.

By the way, I also wrote a command line script for that: Use enrichr enrichment from command line
https://github.com/wdecoster/enrichr_cli

Answer 2

[andrew.j.skelton73]

Reactome is pretty good. OpenTargets is also really really useful, but isn't for pathway analysis (as far as I'm aware).

Answer 3

[Girolamo]

you can also have a look to panther http://pantherdb.org/