Question: Pathway Analysis In R
12
gravatar for Avoks
6.7 years ago by
Avoks140
Avoks140 wrote:

Hi all,

I was wondering if anyone could give some insight into the pathway analysis tools available in R. I would like to run an a pathway analysis to check for significantly enriched pathways using a genelist as the input. I did come across a gene2pathway package that is no longer supported and also a sigPathway tool but this is only available in the dev version of R.

I have read the post about tools to identify significantly altered pathways but it's been almost 10months and I would really appreciate any additional suggestions.

Thanks.

Avoks

pathway gene R • 24k views
ADD COMMENTlink modified 15 months ago by theobroma221.1k • written 6.7 years ago by Avoks140
6
gravatar for Gjain
6.7 years ago by
Gjain5.2k
Göttingen, Germany
Gjain5.2k wrote:

Hi,

KEGGgraph package

is one of R packages which will let you interface between KEGG pathways and graph modeling in R.

Here is the documentation: http://www.bioconductor.org/packages/2.6/bioc//vignettes/KEGGgraph/inst/doc/KEGGgraph.pdf

hope this helps.

ADD COMMENTlink written 6.7 years ago by Gjain5.2k
3

The data in Bioconductor KEGG.db is a snapshot from before the subscription period, and is slowly becoming out-of-date; loading KEGG.db in a recent R / Bioconductor displays a prominent message about this. Other pathway tools work with GO.db, Reactome.db, or arbitrary gene sets. There are also facilities for interaction with Cytoscape.

ADD REPLYlink written 6.7 years ago by Martin Morgan1.5k
1

Is this package affected by the recently required KEGG license subscription? The ftp site referenced int he docs is no longer accessible.

ADD REPLYlink written 6.7 years ago by seidel6.5k

Thanks a bunch, I'll check it out.

ADD REPLYlink written 6.7 years ago by Avoks140
4
gravatar for Sean Davis
6.7 years ago by
Sean Davis24k
National Institutes of Health, Bethesda, MD
Sean Davis24k wrote:

You might check this list, available using the biocViews functionality from Bioconductor:

Pathway BiocViews

Also, sigPathway has been available since R-2.13 at least. Sounds like you might have to upgrade your R installation.

http://bioconductor.org/packages/2.9/bioc/html/sigPathway.html

ADD COMMENTlink modified 6.7 years ago • written 6.7 years ago by Sean Davis24k

Thanks Sean, I now have.

ADD REPLYlink written 6.7 years ago by Avoks140
3
gravatar for montoya.oscar
15 months ago by
montoya.oscar50 wrote:

Take a look at clusterProfiler, DOSE, and STRINGdb packages, all in Bioconductor.

ADD COMMENTlink modified 15 months ago • written 15 months ago by montoya.oscar50
2
gravatar for murphy.charlesj
6.1 years ago by
United States
murphy.charlesj90 wrote:

I've recently come across ReactomePA. Just supply Entrez gene IDs for pathway enrichment analysis using Reactome pathway database.

http://www.bioconductor.org/packages/devel/bioc/html/ReactomePA.html

ADD COMMENTlink modified 6.1 years ago • written 6.1 years ago by murphy.charlesj90
1
gravatar for Qdjm
6.7 years ago by
Qdjm1.9k
Toronto
Qdjm1.9k wrote:

Have you tried the GOstats package in Bioconductor?

ADD COMMENTlink written 6.7 years ago by Qdjm1.9k

No, I haven't but will do. Thanks.

ADD REPLYlink written 6.7 years ago by Avoks140
1
gravatar for Larry_Parnell
6.7 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

I like g:Profiler and the g:GOSt tool, which performs statistical enrichment analysis to provide interpretation of gene lists, using gene ontology terms, biological pathways, regulatory motifs of transcription factors and microRNAs, human disease annotations and protein-protein interactions. I use it via web interface on an occasional basis. I have just noticed that there is an R package available.

ADD COMMENTlink written 6.7 years ago by Larry_Parnell16k

Thanks Larry. I will download the R package and try it out as well.

ADD REPLYlink written 6.7 years ago by Avoks140
1
gravatar for theobroma22
15 months ago by
theobroma221.1k
theobroma221.1k wrote:

If you can get the Entrez IDs for your genelist I recommend the signaling pathway impact analysis aka SPIA bioconductor package.

ADD COMMENTlink written 15 months ago by theobroma221.1k
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