Setup for the BIGapp Workshop

Complete this check before the workshop

Install BIGapp locally, download the example files, and pass the workshop preflight check.
Author

Alexander M. Sandercock

Published

December 14, 2025

Modified

July 13, 2026

Setup at a glance

  • When: complete before the guided session
  • Goal: start BIGapp on your own computer
  • You need: R 4.4.0 or later and internet access for installation
  • Pass condition: the workshop VCF loads in local BIGapp

We will run every workshop analysis in a local BIGapp installation. Installation can take time because BIGapp depends on several R and Bioconductor packages, so complete this page before the guided session.

1. Install R

Install R 4.4.0 or later from the Comprehensive R Archive Network. After installation, open the R console or RStudio and check the version:

R.version.string

If the reported version is older than 4.4.0, update R before continuing.

2. Install BIGapp

In a fresh R session, run the installation commands from the official BIGapp repository:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}
install.packages("remotes")

BiocManager::install(
  "Breeding-Insight/BIGapp",
  dependencies = TRUE
)

R will also install the required dependencies. If it asks whether to update old packages, review the prompt and follow the policy used for your computer or organization.

3. Start BIGapp locally

Run this command in R each time you want to start the application:

BIGapp::run_app()

BIGapp opens in a web browser, but the R process on your computer is doing the analysis. Keep that R session running and leave the console window open.

When you are finished, return to the R console and press Esc in RStudio or Ctrl+C in a terminal.

Confirm that the left navigation includes VCF Filtering, PCA, GWASpoly, Predictive Ability, and Genomic Prediction.

BIGapp home page showing the left navigation and welcome content

BIGapp home page with the main navigation at left.
NoteOnline version is view-only

The public BIGapp preview can be used to look at the interface before installation. It is not the workshop analysis environment. Run every upload, filter, PCA, GWASpoly, and genomic-selection exercise in your local installation.

4. Download the example files

Save all three files in one folder. Do not extract the compressed VCF.

Download Expected contents
Genotype VCF 1,200 variants and 200 samples
Phenotype CSV 200 records plus a header
SNP-information CSV 1,200 records plus a header

The dataset guide provides checksums, field definitions, simulation details, and expected results.

5. Run the required preflight check

  1. Start local BIGapp with BIGapp::run_app() if it is not already running.
  2. In BIGapp, open Genotype Processing and select VCF Filtering.
  3. Under Choose VCF File, browse to atlantic_giant_pumpkin_diversity.vcf.gz.
  4. Wait for the upload progress indicator to finish.
  5. Confirm that the file is accepted without a malformed-VCF message.

The VCF upload completes and the Quality Filtering inputs remain available. You do not need to select Apply Filters yet. This confirms that the required local installation and teaching file are ready.

Troubleshooting

Confirm that the filename still ends in .vcf.gz and that your browser did not rename or extract it. Download the local copy again, restart BIGapp locally, and retry.

Restart R, record R.version.string, and retain the complete installation error. Search existing BIGapp issues before opening a new one. On macOS, compiled dependencies may also require the current Xcode command line tools.

For maintained requirements and release instructions, consult the official BIGapp README.

Next: After the local preflight passes, continue to Module 1: Data quality control.

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