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acs2023_poster

Poster for 2023 Tri-Societies Meeting presenting research on stagewise analysis of perennial breeding trials

agml

AgML is a comprehensive library for agricultural machine learning. Currently, AgML provides access to a wealth of public agricultural datasets for common agricultural deep learning tasks.

apps-phenotyping

The following are scripts and instruction necessary to set up 4 Raspberry Pi Powered Imaging Platforms

barleypheno

An R package to run phenotypic data processing, optimized for the UMN Barley Breeding Group

berrybox

A pipeline for measuring quality traits on cranberries using images of berries in a lightbox

berryhotbox

Code for capturing and analyzing thermal images of berries in a heat chamber

bioinformatic-utils

Script to perform various bioinformatics operations

breeding-notes

Simple repository of links to tools for plant breeding and genetics

cranberryexplorations

Repository for documenting cranberry exploration and collection trips

cranberrygermplasmeaa

cranberryhistoricalgbs

GBS Pipeline for SNP calling in historically genotyped cranberry populations

envirotyping

Pipeline to select environmental covariates for use in plant breeding analysis and prediction

fbutils

Functions to analyze experimental data from the Android Field Book App

fcnworkflow

Repository of template scripts for implementing fully convolutional neural networks for image segmentation

field-book

Field Book

fieldtrial-excel

Function to create a formatted excel file based on a plot design function

finding_berries

PyTorch implementation of the paper "Finding Berries: Segmentation and Counting of Cranberries using Point Supervision and Shape Priors". Peri Akiva, Kristin Dana, Peter Oudemans, Michael Mars. CVPRW2020.

fsimpute

An R package for imputing data from genotyping-by-sequencing experiments in bi-parental populations of finite generations of selfing

gbarleys

A pipeline for handling genotyping-by-sequencing data and calling variants

grass.leaf_rust.detection_2.26.19

Demo showcasing crown and stem rust detection on perennial ryegrass leaves

gs_shiny

A web-app for exploring genomic predictions

gws

A R package for genomic or genomewide selection

heritability

Heritability in plant breeding

ivs_2021_poster

Poster on cranberry environmental association for the 2021 International Vaccinium Symposium

journals

Recent finds in journals covering genetics, genomics, and evolutionary biology.

making-training-data

mixed_model_applications

Examples of using mixed models for plant breeding applications

mxo_geneticmap

Repository supporting the genetic analysis of cranberry interspecific "F2" population

nabrw_2022_poster

Poster on optimizing regional plant breeding nurseries for the 2022 NABRW/BIC meeting

nacrew_2023_poster

Repo for a poster for the 2023 NACREW Conference