Breeding Insight Software https://breeding-insight.github.io/SoftwareHub/news.html Release notes for Breeding Insight software. quarto-1.10.18 Mon, 24 Aug 2026 00:00:00 GMT Familia 2.0.0 https://breeding-insight.github.io/SoftwareHub/news/familia-2.0.0.html
  • Added a Ploidy selector to the Find Parentage and Validate Pedigree tabs, passed through to ‘BIGpopA’ so pedigree validation and parentage assignment now support any ploidy. Even ploidy uses the full polysomic Mendelian test; odd ploidy (e.g. triploid) uses a homozygosity-based check. Default is 2 (diploid).
  • Updated the in-app Instructions and Help panels to document the Ploidy option and to generalize genotype dosage coding to 0, 1, …, ploidy.
  • Requires ‘BIGpopA’ (>= 2.0.0).

    • Release on GitHub · About Familia

    Back to top ]]>     Familia https://breeding-insight.github.io/SoftwareHub/news/familia-2.0.0.html Mon, 24 Aug 2026 00:00:00 GMT     BIGpopA 2.0.0 https://breeding-insight.github.io/SoftwareHub/news/bigpopa-2.0.0.html
  • find_parentage() and validate_pedigree() now support any ploidy through a new ploidy argument (default 2). Genotypes may be coded as allele-B dosage (0, 1, …, ploidy).
  • Even ploidy uses a generalized polysomic gamete-range Mendelian test; it is exact for autopolyploids and conservative for allopolyploids (correct trios are never wrongly flagged).
  • Odd ploidy (e.g. triploid), where balanced gametes are undefined, automatically falls back to a model-free opposite-homozygote exclusion evaluated on homozygous-informative markers only.
  • Diploid results (ploidy = 2) are unchanged from previous versions.

    • Release on GitHub · About BIGpopA

    Back to top ]]>     BIGpopA https://breeding-insight.github.io/SoftwareHub/news/bigpopa-2.0.0.html Thu, 20 Aug 2026 00:00:00 GMT     Familia 1.0.4 https://breeding-insight.github.io/SoftwareHub/news/familia-1.0.4.html
  • Updated the funding attribution banner on the Home tab to read “University of Florida” instead of “Cornell University”, reflecting the correct institution.
  • Added URL and BugReports fields to DESCRIPTION.

    • Release on GitHub · About Familia

    Back to top ]]>     Familia https://breeding-insight.github.io/SoftwareHub/news/familia-1.0.4.html Thu, 13 Aug 2026 00:00:00 GMT     BIGapp 1.8.0 https://breeding-insight.github.io/SoftwareHub/news/bigapp-1.8.0.html

    What’s Changed

    • updated minor edits by @alex-sandercock in https://github.com/Breeding-Insight/BIGapp/pull/150
    • include main updates by @alex-sandercock in https://github.com/Breeding-Insight/BIGapp/pull/152
    • madc2vcf updates by @Cristianetaniguti in https://github.com/Breeding-Insight/BIGapp/pull/154
    • Merge GS-Amat support to development by @alex-sandercock in https://github.com/Breeding-Insight/BIGapp/pull/153
    • Implement UI and madc2vcf updates with GS-Amat support by @alex-sandercock in https://github.com/Breeding-Insight/BIGapp/pull/155

    Full Changelog: https://github.com/Breeding-Insight/BIGapp/compare/v1.6.0…v1.8.0

    Release on GitHub · About BIGapp

    Back to top ]]>     BIGapp https://breeding-insight.github.io/SoftwareHub/news/bigapp-1.8.0.html Tue, 04 Aug 2026 00:00:00 GMT     Familia 1.0.2 https://breeding-insight.github.io/SoftwareHub/news/familia-1.0.2.html *Fixed test directory for CRAN submission

    Release on GitHub · About Familia

    Back to top ]]>     Familia https://breeding-insight.github.io/SoftwareHub/news/familia-1.0.2.html Thu, 09 Jul 2026 00:00:00 GMT     AlloMate 2.1.0 https://breeding-insight.github.io/SoftwareHub/news/allomate-2.1.0.html No release notes were provided.

    Release on GitHub · About AlloMate

    Back to top ]]>     AlloMate https://breeding-insight.github.io/SoftwareHub/news/allomate-2.1.0.html Wed, 03 Jun 2026 00:00:00 GMT     AlloMate 2.0.0 https://breeding-insight.github.io/SoftwareHub/news/allomate-2.0.0.html No release notes were provided.

    Release on GitHub · About AlloMate

    Back to top ]]>     AlloMate https://breeding-insight.github.io/SoftwareHub/news/allomate-2.0.0.html Wed, 03 Jun 2026 00:00:00 GMT     Familia 1.0.0 https://breeding-insight.github.io/SoftwareHub/news/familia-1.0.0.html

    What’s Changed

    • Josue adds by @josuechinchilla in https://github.com/Breeding-Insight/familia/pull/3
    • Add ped cleaner by @josuechinchilla in https://github.com/Breeding-Insight/familia/pull/5
    • Add parentage functions+breedverse panel by @josuechinchilla in https://github.com/Breeding-Insight/familia/pull/6
    • Development by @josuechinchilla in https://github.com/Breeding-Insight/familia/pull/7

    New Contributors

    • @josuechinchilla made their first contribution in https://github.com/Breeding-Insight/familia/pull/3

    Full Changelog: https://github.com/Breeding-Insight/familia/compare/v0.1.0…v1.0.0

    Release on GitHub · About Familia

    Back to top ]]>     Familia https://breeding-insight.github.io/SoftwareHub/news/familia-1.0.0.html Tue, 02 Jun 2026 00:00:00 GMT     BIGr 0.7.2 https://breeding-insight.github.io/SoftwareHub/news/bigr-0.7.2.html
  • Fixed manual text errors

    • Release on GitHub · About BIGr

    Back to top ]]>     BIGr https://breeding-insight.github.io/SoftwareHub/news/bigr-0.7.2.html Mon, 18 May 2026 00:00:00 GMT     BIGapp 1.6.0 https://breeding-insight.github.io/SoftwareHub/news/bigapp-1.6.0.html Improved user warnings and addressed minor bug fixes

    Release on GitHub · About BIGapp

    Back to top ]]>     BIGapp https://breeding-insight.github.io/SoftwareHub/news/bigapp-1.6.0.html Fri, 13 Mar 2026 00:00:00 GMT     BIGapp 1.5.1 https://breeding-insight.github.io/SoftwareHub/news/bigapp-1.5.1.html 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

    Release on GitHub · About BIGapp

    Back to top ]]>     BIGapp https://breeding-insight.github.io/SoftwareHub/news/bigapp-1.5.1.html Tue, 23 Sep 2025 00:00:00 GMT     BIGr 0.6.2 https://breeding-insight.github.io/SoftwareHub/news/bigr-0.6.2.html
  • Fixed the doi and name list in the CITATION file

    • Release on GitHub · About BIGr

    Back to top ]]>     BIGr https://breeding-insight.github.io/SoftwareHub/news/bigr-0.6.2.html Thu, 18 Sep 2025 00:00:00 GMT     BIGapp 1.3.0 https://breeding-insight.github.io/SoftwareHub/news/bigapp-1.3.0.html 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.

    Release on GitHub · About BIGapp

    Back to top ]]>     BIGapp https://breeding-insight.github.io/SoftwareHub/news/bigapp-1.3.0.html Wed, 04 Jun 2025 00:00:00 GMT     BIGr 0.5.5 https://breeding-insight.github.io/SoftwareHub/news/bigr-0.5.5.html
  • Updated DESCRIPTION
  • Added return value for merge_MADCs
  • Added optional seed for check_ped
  • Added verbose option

    • Release on GitHub · About BIGr

    Back to top ]]>     BIGr https://breeding-insight.github.io/SoftwareHub/news/bigr-0.5.5.html Mon, 19 May 2025 00:00:00 GMT     BIGapp 1.2.0 https://breeding-insight.github.io/SoftwareHub/news/bigapp-1.2.0.html 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

    Release on GitHub · About BIGapp

    Back to top ]]>     BIGapp https://breeding-insight.github.io/SoftwareHub/news/bigapp-1.2.0.html Thu, 27 Mar 2025 00:00:00 GMT     BIGr 0.4.2 https://breeding-insight.github.io/SoftwareHub/news/bigr-0.4.2.html
  • Minor update to the check_ped() function

    • Release on GitHub · About BIGr

    Back to top ]]>     BIGr https://breeding-insight.github.io/SoftwareHub/news/bigr-0.4.2.html Tue, 18 Mar 2025 00:00:00 GMT     BIGr 0.4.1 https://breeding-insight.github.io/SoftwareHub/news/bigr-0.4.1.html Minor bug fixes

    Release on GitHub · About BIGr

    Back to top ]]>     BIGr https://breeding-insight.github.io/SoftwareHub/news/bigr-0.4.1.html Fri, 07 Mar 2025 00:00:00 GMT     BIGapp 1.1.0 https://breeding-insight.github.io/SoftwareHub/news/bigapp-1.1.0.html 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

    Release on GitHub · About BIGapp

    Back to top ]]>     BIGapp https://breeding-insight.github.io/SoftwareHub/news/bigapp-1.1.0.html Fri, 21 Feb 2025 00:00:00 GMT     BIGr 0.4.0 https://breeding-insight.github.io/SoftwareHub/news/bigr-0.4.0.html New functions and bug fixes: - get_offTargets: obtain the target and off-target SNPs from a fixedAllele MADC file - madc2vcf: obtain the read count information for target SNPs only from a fixedAllele MADC file and convert to VCF format

    Release on GitHub · About BIGr

    Back to top ]]>     BIGr https://breeding-insight.github.io/SoftwareHub/news/bigr-0.4.0.html Thu, 20 Feb 2025 00:00:00 GMT     BIGr 0.3.4 https://breeding-insight.github.io/SoftwareHub/news/bigr-0.3.4.html
  • Bug fixes

    • Release on GitHub · About BIGr

    Back to top ]]>     BIGr https://breeding-insight.github.io/SoftwareHub/news/bigr-0.3.4.html Sat, 28 Dec 2024 00:00:00 GMT