GO categories in R for A. Thaliana
1
0
Entering edit mode
@vishal-thapar-3427
Last seen 7.1 years ago
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 GO Arabidopsis thaliana • 1.3k views
ADD COMMENT
0
Entering edit mode
Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 5.2 years ago
United States
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 COMMENT
0
Entering edit mode

 Hi Everyone,

How to pathway analysis of Arabidopsis thaliana organism using  pathview.

Data  preparation for input and analysis.

thank you

ADD REPLY

Login before adding your answer.

Traffic: 300 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6