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Arabidopsis EcoGEx (R-📦 + 🕸️-App)
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README.md

EcoGEx : Ecotype-specific Gene Expression (R-📦 + 🕸️-App)

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If this helps you please cite: DOI

Quick Start

EcoGEx Web instance can be accessed - here

Install the package and run the shiny app locally

require(devtools)
devtools::install_github("sk-sahu/EcoGEx")

To run EcoGEx instance locally:

library(EcoGEx)
runEcoGEx()

About

Arabidopsis EcoGEx is a shinny web app to find Expression of a Gene across different accessions/strains of Arabidopsis and their geographical locations information of origin.

By simply using an AGI (Arabidopsis Gene Identifier) you can look at their Expression pattern and also can Compare between diffrent accessions.

Here is an example of some graphical outputs from the results after running the app:


If you have an idea for improvement or found a bug then please raise an issue.
Or simply email on: sangramk@iisermohali.ac.in


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Why this package/app when one can go over available set of large Excel files and dig out the information? Because, recently I came across this tweet of Hadley Wickham, which insipred me to write my first full fledged code (Well, atleast in my mind!).

Automate everything that can be automated. I had to work hard to make it easier for others

— Hadley Wickham (@hadleywickham) September 24, 2017

And this also mentioned as his phillospohy of package development in his book Introduction to R-packages

Anything that can be automated, should be automated.

I know this code in production is not perfect. Most functions are messy and lot of improvements to do, but the idea of MVP can lead.


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