This project has been made to simplify the work of biologists when they are studying the rice genome. The aim of this project is to support analysis of the rice genomics, including the downstream analysis of GWAS such as gene annotation, QTL analysis and primer design.
This rRice package will allow the biologist to :
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Create an experiment.
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Interrogate Databases. Currently, 10 databases are avaible to use :
- RAPDB (http://rapdb.dna.affrc.go.jp/)
- Gramene (http://www.gramene.org/)
- Oryzabase (https://shigen.nig.ac.jp/rice/oryzabase/)
- IC4R (http://ic4r.org/)
- PlantTFDB (http://planttfdb.cbi.pku.edu.cn/)
- PlnTFDB (http://plntfdb.bio.uni-potsdam.de/)
- Funricegenes (https://funricegenes.github.io/docs/)
- Funricegenes2
- Funricegenes3
- MSU7 (http://rice.plantbiology.msu.edu/)
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Add manually new databases to your experiment in order to enrich your datas.
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Create an array with only the genes and properties wanted.
The installation of the rRice package will require few tools on your computer :
- R
- Python3 with few libraries available (
pandas,requests,bs4,json,gzipandlxml)
If you want to install rRice package you will have to follow the instructions below :
To install rRice package, start R and enter write the following lines :
source("https://bioconductor.org/biocLite.R")
biocLite("rRice")
The rRice package is licenced under the Artistic-2.0