Question: pathway analysis tools and KEGG gene sets from MSigDB
1
gravatar for Zhilong Jia
4.3 years ago by
Zhilong Jia1.4k
London
Zhilong Jia1.4k wrote:

Is there other pathway analysis tools except GSEA using gene set from MSigDB database? For example, tools can use user-defined pathway gene set or support gene set (gmt) from MSigDB directly? Thank you.

kegg pathway analysis msigdb • 4.6k views
ADD COMMENTlink modified 12 months ago by Biostar ♦♦ 20 • written 4.3 years ago by Zhilong Jia1.4k
9
gravatar for Deepak Tanwar
4.3 years ago by
Deepak Tanwar4.0k
ETH Zürich, Switzerland
Deepak Tanwar4.0k wrote:

You could use qusage http://clip.med.yale.edu/qusage/

This is a Bioconductor package and is easy to use with R.

You could also use the piano http://www.bioconductor.org/packages/release/bioc/html/piano.html

This is also a Bioconductor package and easy to use. 

Go through the manuals and try to follow steps with the given examples.

 

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Deepak Tanwar4.0k
1
gravatar for ddiez
2.9 years ago by
ddiez1.8k
Japan
ddiez1.8k wrote:

You can also use MSigDB gene set data with the gene set tools in the limma package (also found in edgeR package if you are analyzing NGS data using GLMs). Tools like camera(), roast(), romer(), etc., all can use gene sets, like those defined in MSigDB. You can download MSigDB gene sets in an R friendly format from the limma/edgeR developer's website here. Take a look at help("10.GeneSetTests") in the limma documentation. Some examples are shown also in the limma and edgeR user's guide.

ADD COMMENTlink written 2.9 years ago by ddiez1.8k
0
gravatar for Guangchuang Yu
2.9 years ago by
Guangchuang Yu2.2k
China/Guangzhou/Southern Medical University
Guangchuang Yu2.2k wrote:

another option in R is using clusterProfiler package.

ADD COMMENTlink written 2.9 years ago by Guangchuang Yu2.2k
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