Protocols

Many of the protocols we use are available from the links below, hopefully you will find them quite helpful.



Arabidopsis CLIMtools
David


David

ExE

AraCLIM

Environment by Environment

David

ExG

CLIMGeno

Climate by Genotype

David

PxE

PhenoCLIM

Phenotype by Environment

David

GxE

GenoCLIM

Genotype by Environment


David
FDRCLIM
FDR control of ExG and ExG associations


Coincidentally, this project ended up having a similar name to a another project by Dr. Dimitrios Gyalistras, ClimTools. All Arabidopsis CLIMtools code is available on our GitHub Repository.

Software

StructureFold2 is our signature bioinfomatic tool to analyze in vivo RNA- structuromes using chemically probed RNA libraries. It is currently hosted on GitHub and frequently updated. Included on GitHub is an easy to follow manual!


StructureFold2 Dependencies



We highly reccomend learning and using Python for most common bioinformatic tasks, where it is a versitile, easy to learn scripting language, with a fully developed host of resources for both novice and enthusiast alike.



R

We highly reccomend learning and using R for all statistical needs, as well as chart and graph generation. R has an almost endless variety of packages, custom-tailored for almost any sort of analysis, while its graphical prowess is almost unmatched.



Scientific Links

Arabidopsis Information Portal (Araport)



The Arabidopsis Information Resource (TAIR)



Nottingham Arabidopsis Stock Centre (uNASC)



The Salk Institute Genomic Analysis Laboratory



National Center for Biotechnology Information Site



Online Analytical Tool link pages



Other