GitHub

127.0.0.1

Welcome to the tutorials for the BIGapp! This application is brought to you by Breeding Insight. BI is an initiative funded by the USDA-ARS and housed at Cornell University. Our mission is to help USDA-ARS breeders transform breeding by enabling the implementation of genomic insight and selection

as part of routine specialty crop and livestock breeding. The creation of the BIGapp is one such tool we believe will help the species we work with streamline breeding decisions. The BIGapp is designed to assist breeding programs in performing some of their own routine genomic analysis. 

If you have any questions or concerns as you use the BIGapp or go through these training modules, please reach out to Breeding Insight at 

. The information shared in these tutorials assist a user in walking through each analysis section step-by-step. For more in-depth information regarding the parameters and result descriptions for each section, visit the in-app help pages described below.

Please note that Scribe materials automatically open a new browser window when a user clicks on specific content. To return to the main training page (this page), simply close the other browsers when complete and keep this main page open.

Important: Please do not refresh your browser while in the BIGapp. Users are able to run various modules or analyses subsequently without losing access to saving and downloading their results. IE: genomic diversity then navigate to do GWASpoly analysis. However, refreshing your browser will result in lost analysis.

 that can be found on the Breeding Insight Github page can only process small amounts of data as it is a demo instance. In order to run increased data sets, please see the "downloading and starting the BIGapp" instructions for Mac Users below.

Mac Users: Install BIGapp using devtools from Github

Mac Users: Starting BIGapp

In-App Help Documentation

Convert to VCF file

Dosage Calling

VCF Filtering

Genomic Diversity

GWASpoly

Predictive Ability

Genomic Prediction

Thank you for reviewing these training modules on BIGapp. If you find that you have any questions or concerns, please reach out to 

BIGapp

Breeding Insight

BIGapp Tutorials

This guide provides a comprehensive walkthrough for utilizing the Predictive Ability feature in the BIGapp. It outlines the process of uploading files, selecting traits, and running analyses, while also highlighting advanced options for more tailored results.

This guide provides essential instructions for analyzing genomic diversity using the BIGapp. It walks users through the process of uploading and analyzing VCF files, selecting species ploidy, and interpreting results through various plots and tables. Additionally, it offers tips on saving images and files, as well as accessing in-app help and example files for a deeper understanding.

This training module walks users through accessing the "help" pages within the BIGapp to learn more about it's various features, results descriptions and how to cite if using BIGapp for publications.

This guide provides step-by-step instructions on how to filter VCF data with specific parameters through the BIGapp. By following these steps, users can easily navigate to the website, input their VCF file, set filtering parameters such as ploidy and missing data thresholds, and generate filtered VCF files for download.

This guide provides a comprehensive overview of the Genomic Prediction feature in the BIGapp, enabling users to effectively analyze genetic data. By following the outlined steps, users can upload relevant files, select traits, and run analyses to obtain predicted phenotypes and estimated breeding values. Additionally, the guide highlights advanced options and resources for further exploration, making it a valuable tool for anyone looking to enhance their understanding of genomic prediction.

This guide offers a step-by-step process for performing dosage calling, a crucial task for analyzing genetic data efficiently. By following this guide, users can streamline their workflow and ensure accurate results in their genetic analyses.

This guide provides step-by-step instructions on how to perform Principal Component Analysis (PCA) on a VCF file. It explains how to upload the file, select parameters, customize the plot, and save the results. The guide also offers tips on color options and provides options for colorblind-friendly plots.

This guide walks a user through launching the BIGapp on a Mac. Note that the BIGapp will soon be available through an online version. Until then, Breeding Insight recommends using a Mac computer and running R through the Terminal.

This guide provides a step-by-step approach to conducting Genome-Wide Association Studies (GWAS) using the GWASpoly tool, making it accessible for users at various skill levels. It offers insights into selecting files, configuring analysis parameters, and interpreting results effectively, including QTL analysis and visualization options.

This guide provides a straightforward process for Mac users to install the BIGapp software via R and GitHub, making it accessible for those interested in utilizing this tool. By following the simple steps, users can efficiently set up the app and access its features in a web browser. It is particularly useful for individuals looking to enhance their data analysis capabilities without extensive technical knowledge.

This guide explains how to convert genotyping reports to VCF files. It provides step-by-step instructions on uploading the necessary files, specifying output file name and species ploidy, running the analysis, and downloading the VCF file.

BIGapp Tutorials

Downloading and starting the BIGapp

Mac Users: Install BIGapp using devtools from Github

Mac Users: Starting BIGapp

Information

In-App Help Documentation

Genotype Processing

Convert to VCF file

Dosage Calling

VCF Filtering

Summary Metrics

Genomic Diversity

Population Structure

PCA

GWAS

GWASpoly

Genomic Selection

Predictive Ability

Genomic Prediction