Assmann Lab presents

Arabidopsis CLIMtools

Created by Ángel Ferrero-Serrano and Sally Assmann

Please cite: Ferrero-Serrano Á, Assmann SM. 2019
Phenotypic and genome-wide association with the local environment of Arabidopsis.
Nature Ecology and Evolution. PMID:30643246, doi: 10.1038/s41559-018-0754-5

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
Protocols

Some of the protocols we use are available from the links below.

Software

StructureFold2 is our signature bioinformatic 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, as it is a versitile, easy to learn scripting language, with a fully developed host of resources.



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.

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

PennState