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agriutilities

analysis-pipeline

aria2.0

Automated Root Imaging Analysis 2.0

asreml-r-short-course

Course notes and scripts from ASReml-R short course taught by Salvador Gezan at the USDA-ARS station in Miami, FL

barcodelabel

A shiny app to generate labels with barcpdes

barnswallow

bison-fly

Bison-Fly is the NDSU Spring Wheat UAV Pipeline developed in partnership with Drone2Phenome UAV community (D2P). In this pipeline we are presenting step by step how we have been applying UAV data on our breeding program. This is a open source R code from where anyone can use and adept for different crops. All suggestions are welcome. Help us to build this platform in partnership with Drone2Phenome community.

bison-fly_workshop_01

Workshop presented at the 2022 NAPPN Annual Conference in Athens, Georgia. In this course, I present step-by-step how we leverage UAV data in our breeding program. This is open source R code that anyone may use and adopt for different crops and situations. The Bison-Fly tutorial is the NDSU Spring Wheat UAV Pipeline developed in partnership with Drone2Phenome (D2P). We hope this pipeline helps you with your research, and all suggestions to improve it are welcome.

blups_heritability

bnagwas

GWAS platform for core collection of Brassica napus

brassica-snps

Scripts for bulk segregant analysis and genotyping of Brassica (T1000 & Jersey Kale)

bsa

Bulked-Segregant Analysis using vcf file with or without parents

cau_phd_scripts

combine_gwas_results_from_gapit

R script that combines all GWAS results for all traits generated by GAPIT and writes two files, one with all marker info and one with marker info for significantly associated markers only.

cop-ciat

cqprot-003

data-science

My notes pertaining to python programming, data analysis and visualization

dh-production-gs

Genomic selection to optimize the doubled haploids-based maize hybrid breeding

draw-plots-qgis

Plugins to draw field experiment plots using R scripts in QGIS

drone-data-in-agricultural-research

Lessons on working with multispectral drone based data in agricultural research settings

drybean_multienvtrials

easympe

Easy micro-plot extraction: a pre-processing tool to extract quality micro-plot images for UAV-based high-throughput field phenotyping

emmax-pipeline

GWAS analysis process based on EMMAX software

fieldhub

FielDHub is an R Shiny design of experiments (DOE) app that aids in the creation of traditional, unreplicated, augmented and partially-replicated designs applied to agriculture, plant breeding, forestry, animal and biological sciences.

fieldimager

FIELDimageR: A R package to analyze orthomosaic images from agricultural field trials. This package is a compilation of functions to analyze pos-mosaicking images from research fields, and allows to: crop the image; remove soil effect; build vegetation indices; rotate the image; build the plot shapefile; extract information for each plot; and evaluate stand count, canopy percentage, and plant height.

fieldimager-workshop-10

Workshop presented for NAPB. In this course, I went through the basic steps of the FIELDimageR pipeline showing how to evaluate and apply remote sensing data in plant breeding.

fxaf1gs

gapit3

Genome Association Predict Integrate Tools

gemma-gwas-scripts

A collection of scripts to aid mixed linear model based GWAS with GEMMA (https://github.com/genetics-statistics/GEMMA)

genesis

GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness