Manigben's repositories
admixture_pie_chart_map_tutorial
Tutorial for visualising admixture on a map
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
Supplementary-File-1
Prediction using temporal phenotype data
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
EasyMPE
Easy micro-plot extraction: a pre-processing tool to extract quality micro-plot images for UAV-based high-throughput field phenotyping
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.
GerminaR
Packages for graphics and index for seed germination ecophysiological evaluation
GPB_250SoyReseq
Scripts used in the GPB article of 250 soybean resequencing
Heritability
Heritability in plant breeding - R and SAS code examples
IBSA
software for BSA-seq based on PyQt
metan
Package for multi-environment trial analysis
meteostat-python
Access and analyze historical weather and climate data with Python.
MrBeanApp
Web application
pbst
Plant Breeding Selection Tools
pliman
Tools for Plant Image Analysis
PyBSASeq
A novel algorithm for BSA-Seq data analysis
S2MET_GSTrainingDesign
Scripts to replicate analysis of using environmental similarities when designing genomewide prediction training set.
statgenGWAS
See https://biometris.github.io/statgenGWAS/index.html for a full description
statgenSTA
See https://biometris.github.io/statgenSTA/index.html for a full description
StructuRly
Comprehensive, detailed and interactive plots for STRUCTURE and ADMIXTURE population analysis
VBA_Toolkit
ICARDA VBA Toolkit for Excel