Question: Genes to human phenotype ontologies
0
gravatar for muhasif123
3.5 years ago by
muhasif1230
Portugal
muhasif1230 wrote:

I am looking for a R package or tool to find human phenotype ontologies (HPO) for a list of genes using semantic methods. I saw one paper 

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115692

where they wrote a R package, namely HPOSim. But I am unable to load it.

Do you know some other R packages like HPOSim or tools? or some has used HPOSim package?

Thanks

 

hpo semantic similarity • 1.4k views
ADD COMMENTlink modified 3.1 years ago by buske0 • written 3.5 years ago by muhasif1230
0
gravatar for Giovanni M Dall'Olio
3.5 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

What error do you get when you load HPOSim? If you can't use the package it would be nice of you to write to the authors and ask them to fix it.

In alternative, I used DOSE which allows to do enrichment on Disease Ontology. Not sure how much it is different from HPO.

ADD COMMENTlink written 3.5 years ago by Giovanni M Dall'Olio26k
0
gravatar for muhasif123
3.5 years ago by
muhasif1230
Portugal
muhasif1230 wrote:

I solved the HPOSim problem. But it didn't work for my problem. Is there any package or tool with wich I can find genes for disease symptoms?

thanks

ADD COMMENTlink written 3.5 years ago by muhasif1230
0
gravatar for buske
3.1 years ago by
buske0
buske0 wrote:

It's not quite what you're asking, but you can download known HPO-gene associations computed by the HPO team from their download page (genes_to_phenotype.txt and phenotype_to_genes.txt).

ADD COMMENTlink written 3.1 years ago by buske0
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