Question: Looking for recommendations of R package for GO enrichment analysis based on gene list and a Trinotate report
0
gravatar for BioBing
2.7 years ago by
BioBing120
Denmark
BioBing120 wrote:

Hi all,

I was wondering if some of you could recommend me a good R package for GO Enrichment Analysis and creating graphs of functional gene clusters?

The data I want to use in the analysis:

1) A Trinotate annotation report that includes GO-ids/terms for each annotated gene

2) A list of genes that I want to analyze (for instance all up regulated genes in a specific treatment originating from differential gene expression analysis of RNAseq data)

Thank you!

Birgitte

go rna-seq trinotate R • 1.3k views
ADD COMMENTlink modified 2.7 years ago by Satyajeet Khare1.5k • written 2.7 years ago by BioBing120
3
gravatar for Satyajeet Khare
2.7 years ago by
Satyajeet Khare1.5k
Pune, India
Satyajeet Khare1.5k wrote:

Have you tried clusterProfiler? I recently used to make compareCluster plots and gseaplot for up and down regulated genes in my analysis. Please refer to its manual here. Its a fairly straightforward to use.

ADD COMMENTlink written 2.7 years ago by Satyajeet Khare1.5k

Thanks! I will check it out!

ADD REPLYlink written 2.7 years ago by BioBing120
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1886 users visited in the last hour