The most popular Alternative to David?
3
1
Entering edit mode
6.0 years ago
bxia ▴ 180

David is down currently?

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

Thanks

RNA-Seq • 5.0k views
ADD COMMENT
0
Entering edit mode

Does it support zebro fish?

ADD REPLY
1
Entering edit mode
ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode

EagleEye participates here regularly and should be along to help.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
1
Entering edit mode
ADD REPLY
0
Entering edit mode
ADD REPLY
0
Entering edit mode

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

ADD REPLY
3
Entering edit mode
6.0 years ago

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

ADD COMMENT
0
Entering edit mode
6.0 years ago

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

ADD COMMENT
0
Entering edit mode
6.0 years ago
Girolamo ▴ 140

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

ADD COMMENT

Login before adding your answer.

Traffic: 1214 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6