v1.5.1

This release includes bug fixes and new feature updates:

• Genotype files are now validated for proper formatting when uploaded
• The correct Ref and Alt bases are retained in the VCF through the genotype processing steps
• The list of removed samples is provided in the VCF Filtering tab

v1.3.0

Introduced several feature updates and bug fixes for BIGapp including documentation improvements, enhanced data processing and visualization options, and updated UI text.

• Updated help file documentation with clearer examples and formatting.
• Enhanced data conversion in dosage2vcf with revised input validations and updated function calls, and improved PCA plotting with added shape options and dynamic aesthetics.
• Minor UI and version updates in home, GSAcc modules, and the application descriptor.

v1.2.0

Feature updates and bug fixes:

• When a trait file is uploaded the user is prompted to select the missing data variable, and select the column containing the sample IDs
• Updated the VCF Filtering tab to allow sample subsetting in the Advanced Options
• Added option to subset samples for the PolyRAD dosage calling method
• Added support for genotype matrix to VCF conversion
• Fixed a UI bug when extracting target SNPs from MADC file
• Added new user warnings to PCA tab

v1.1.0

This includes many feature updates - including:

• The ability to get target + off-target SNPs from MADC files
• Support added for PolyRAD dosage calling (this is 100x faster than Updog at the expense of slightly more memory usage)
• Support for SVG figure download
• Export VCF as bgzipped files for interoperability with other tools
• UI improvements and bug fixes

This version will require R 4.4.0

v1.0.0

This full public release of BIGapp includes:

• Bug fixes
• Updated genomic selection methods to use relationship matrices
• Improved error handling
• Updated GWAS functions
• Updated PCA figure customization
• Improved Help tab information and links within each analysis tab
• Updated UI to be more consistent throughout

v0.6.1-beta

-Minor bug fixes

v0.6.0-beta

Bug fixes and feature enhancements:

• Updated Dosage Calling tab to allow user to subset genotyping data and select parental genotypes depending on Updog model
• Genomic Selection can now use pedigree information for generating the relationship matrices

v0.5.0-beta

• Original code was updated into the R Golem format
• System checks added
• Improved app stability
• New user warnings
• Updates to UI
• New plot added to PCA tab
• New Genomic Selection tab

v0.3.0

• Updated all analyses to use VCF
• Added VCF filtering functions
• Added ability to convert from DArT Dose Report and Counts files to VCF
• Updated Genomic Prediction analysis to use 5-fold cv
• Bug fixes for PCA figures

v0.2.0-alpha: Multiple Updates

• Added DAPC analysis tab
• Combined DAPC and PCA under a common "Population Structure" tab
• Updated the BIG logo