Question: GO categories in R for A. Thaliana
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gravatar for Vishal Thapar
10.4 years ago by
Vishal Thapar90 wrote:
Dear Listers, I had a small query. I am working with A. Thaliana and after some initial analysis I have a list of genes (2000 or so). I want to now classify them into GO categories. I know there are lots of web based tools to do this but I want to do this in R. Has anyone done this before ? (I am sure, someone has, or so I hope) I tried to look around but I didn't find any whole genome annotation package like "org.Hs.eg.db" for Arabidopsis Thaliana. I found this on BioC http://bioconductor.org/packages/2.2/Arabidopsis_thaliana.html But it does not seem like I can use this for my GO term analysis. Does anyone know of a package in R that can be used for Arabidopsis? Any pointers and help would be greatly appreciated. Thanks, Sincerely, Vishal -- Vishal Thapar, Ph.D. Post Doctoral Researcher Cold Spring Harbor Lab Williams #5, 1 Bungtown Road Cold Spring Harbor, NY - 11724 [[alternative HTML version deleted]]
go arabidopsis thaliana • 1.1k views
ADD COMMENTlink modified 10.4 years ago by Marc Carlson7.2k • written 10.4 years ago by Vishal Thapar90
Answer: GO categories in R for A. Thaliana
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gravatar for Marc Carlson
10.4 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Hi Vishal, We have an organism level package for Arabidopsis in the development branch: http://www.bioconductor.org/packages/devel/data/annotation/html/org.At .tair.db.html Please let us know if you find it satisfactory or not (it's new). Also, if you have general question about GO ontologies, you might want to look at the basic GO usage vignette here: http://www.bioconductor.org/packages/devel/bioc/html/annotate.html And if you want to do some hypergeometric testing you might want to look at the GOstats package: http://www.bioconductor.org/packages/devel/bioc/html/GOstats.html Hope this helps, Marc Vishal Thapar wrote: > Dear Listers, > > I had a small query. I am working with A. Thaliana and after some initial > analysis I have a list of genes (2000 or so). I want to now classify them > into GO categories. I know there are lots of web based tools to do this but > I want to do this in R. Has anyone done this before ? (I am sure, someone > has, or so I hope) I tried to look around but I didn't find any whole genome > annotation package like "org.Hs.eg.db" for Arabidopsis Thaliana. I found > this on BioC > http://bioconductor.org/packages/2.2/Arabidopsis_thaliana.html > But it does not seem like I can use this for my GO term analysis. Does > anyone know of a package in R that can be used for Arabidopsis? Any pointers > and help would be greatly appreciated. > > Thanks, > > Sincerely, > > Vishal > >
ADD COMMENTlink written 10.4 years ago by Marc Carlson7.2k

 Hi Everyone,

How to pathway analysis of Arabidopsis thaliana organism using  pathview.

Data  preparation for input and analysis.

thank you

ADD REPLYlink written 2.7 years ago by avinash gupta130
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