https://github.com/breeding-insight/bigapp - 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.

- R
Published by alex-sandercock about 1 year ago

https://github.com/breeding-insight/bigapp - 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

- R
Published by alex-sandercock about 1 year ago

https://github.com/breeding-insight/bigapp - 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

- R
Published by alex-sandercock over 1 year ago

https://github.com/breeding-insight/bigapp - 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

- R
Published by alex-sandercock over 1 year ago

https://github.com/breeding-insight/bigapp - v0.6.1-beta

-Minor bug fixes

- R
Published by alex-sandercock over 1 year ago

https://github.com/breeding-insight/bigapp - 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

- R
Published by alex-sandercock over 1 year ago

https://github.com/breeding-insight/bigapp - 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

- R
Published by alex-sandercock almost 2 years ago

https://github.com/breeding-insight/bigapp - 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

- R
Published by alex-sandercock almost 2 years ago

https://github.com/breeding-insight/bigapp -

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

- R
Published by alex-sandercock about 2 years ago

https://github.com/breeding-insight/bigapp - Initial release

This is the initial release for the BIG app. Several analysis tabs are still in development.

- R
Published by alex-sandercock about 2 years ago