Question

Joint pathway Analysis using both gene and metabolite data sets

0

Entering edit mode

emisecherre • 0

@emisecherre-23089

Last seen 4.4 years ago

Hello !

I'm looking for an API or package which can perform a joint pathway analysis using a list of genes and a list of metabolites at least. My aim would be to find pathways which include as many items of my lists as possible.

Thanks in advance !

data integration gene metabolite • 1.2k views

ADD COMMENT • link 4.8 years ago emisecherre • 0

score 1 · Answer 1 · 2020-03-13

1

Entering edit mode

James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 2 days ago

United States

The mogsa package comes to mind.

ADD COMMENT • link 4.8 years ago James W. MacDonald 67k

score 1 · Answer 2 · 2020-03-13

1

Entering edit mode

Kevin Blighe ★ 4.0k

@kevin

Last seen 5 weeks ago

Republic of Ireland

MetaboAnalyst is another that comes to mind, but this is a web interface.

Kevin

ADD COMMENT • link 4.8 years ago Kevin Blighe ★ 4.0k

score 0 · Answer 3 · 2020-03-13

0

Entering edit mode

svlachavas ▴ 840

@svlachavas-7225

Last seen 14 months ago

Germany/Heidelberg/German Cancer Resear…

You could also try MOFA:

https://bioconductor.org/packages/release/bioc/html/MOFA.html

ADD COMMENT • link 4.8 years ago svlachavas ▴ 840

score 0 · Answer 4 · 2020-03-16

0

Entering edit mode

emisecherre • 0

@emisecherre-23089

Last seen 4.4 years ago

okay i'll try them, thank you all !

ADD COMMENT • link 4.8 years ago emisecherre • 0