neyhartj

pbsim

An R package of functions to perform breeding simulations.

qgshiny

A Shiny App for teaching introductory quantitative genetics

BerryBox

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

bioinformatic-utils

Script to perform various bioinformatics operations

envirotyping

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

mixed_model_applications

Examples of using mixed models for plant breeding applications

StageWise

two-stage analysis of multi-environment trials for genomic selection and GWAS

statgenSTA

See https://biometris.github.io/statgenSTA for a full description

breeding-notes

Simple repository of links to tools for plant breeding and genetics

neyhart

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

BerryHotBox

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

CranberryExplorations

Repository for documenting cranberry exploration and collection trips

CranberryGermplasmEAA

cranberryHistoricalGBS

GBS Pipeline for SNP calling in historically genotyped cranberry populations

FCNWorkflow

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

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.

GBarleyS

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

gws

A R package for genomic or genomewide selection

IVS_2021_Poster

Poster on cranberry environmental association for the 2021 International Vaccinium Symposium

NACREW_2023_Poster

Repo for a poster for the 2023 NACREW Conference

neyhart-lab-website

Source code for the Neyhart Lab website

neyhartj

Config files for my GitHub profile.

potato_seed.ct_8.7.20

programming_notes

Notes for various programming examples

Rtutorials

Repository of R programming tutorials and examples

selectiongain2

Modification of the R package selectiongain

snps

An R package with utility functions for manipulating SNP marker data.