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aradeepopsis
A versatile, fully open-source pipeline to extract phenotypic measurements from plant imagesmlmm
An efficient multi-locus mixed-model approach for genome-wide association studies in structured populationsbookend
End-guided RNA assemblerTRG-ImageProcessing
Swarts Lab CNN stuffMultLocMixMod
An efficient multi-locus mixed-model approach for genome-wide association studies in structured populationsSNPmatch
A simple python library to identify the most likely strain from the populationmtmm
A mixed-model approach for genome-wide association studies of correlated traits in structured populationstissue-enrichment-test
GWA-Portal
Web-app to store an display GWAS studiesgwaR
A collection of R functions to conduct downstream GWAS analysis for arabidopsis thaliana.PhenoBox-System
The โPhenoboxโ, a flexible, automated, open-source plant phenotyping solutionisoseq3
dormancy
Dormancy Paper infosswedish-genomes
Massive genomic variation and strong selection in Arabidopsis thaliana lines from SwedensRNA-spike-ins
Contains scripts used to design and analyze small RNA spike-in oligonucleotides as described in Lutzmayer, Enugutti and Nodine (2017) Novel small RNA spike-in oligonucleotides enable absolute normalization of small RNA-Seq data, Scientific ReportsScanPlateSeg
Python scripts for detection and alignment of dish in scanned seedling datavbc-cicd-examples
examples for container builds at VBCPlotnikova.2019
Custom software used to analyze data and generate figures for Plotnikova et al. (2019, Plant Cell)env_init
Linux Environment Initialisation scripts for Scientific Computing on HPC and Workstation DeploymentsnanoPARE
RNA 5' analysis tools for use with the nanoPARE protocolpyBsHap
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