Hello problem solver!
Your message is already clear, but I've made a few adjustments for grammar and flow:
I have obtained some DEGs from a single-cell transcriptomic analysis of rice samples. Currently, I am trying to perform gene ontology using bioMart goseq in R.
However, I am facing challenges while introducing R to the rice dataset and genome from EnsemblPlants. I cannot find a library for rice genome annotation to connect in R. For instance, there is a library available for the human genome - org.Hs.eg.db - but not for rice!
Could you please assist me in finding the rice (Oryza sativa japonica group) genome annotation link to connect in R? This would enable R to access information about gene IDs and gene/transcript lengths of my DEGs from the rice genome and, ultimately, provide me with GO annotation.
I have been working on this task for quite some time, and I even dedicated this weekend to the GO analysis! Now, I am eager to complete it as soon as possible!!!
Your valuable comments are truly appreciated!
Best,
Sadia Prity
First year Ph.D. study
I don't see anything in Bioconductor like an org.db for rice other than
MeSH.Osa.eg.dbwhich appears to be deprecated. I think you'll have to provide gene id to GO term mappings by compiling that data from a different source. Have you triedbiomaRtto pull GO accessions connected to your gene ids?Thank you so much for your response. Actually I dont find any sources for rice annotation to use in R. I will try biomaRt for GO accessions as you suggested. Thanks again! :)