NEWS
geneNR 3.0.0 (2026-07-05)
Major Changes and Enhancements
- Offline Local GFF3 Engine: Added complete support for custom local assemblies via
genome_source = "local". Users can now pass a path to a .gff3 file using the gff3_file parameter, enabling completely offline and highly flexible genome lookups.
- Robust Fallback Validation Framework: Integrated an internal mock genomic database (
sample_crop.gff3) that automatically handles coordinate mapping when local mode is selected without a file path, ensuring out-of-the-box functionality.
- Online and Offline Efficiency: Re-engineered the underlying data routing structure across
geneSNP(), geneQTL(), and geneSNPcustom(). The package now safely balances real-time web-scraping from Ensembl Plants and ultra-fast local coordinate intersections.
geneNR 2.0.1 (2025-03-29)
New Functions and Features
geneQTL: Identifies candidate genes based on Quantitative Trait Loci (QTL) analysis.import_hmp: Enables importing Hapmap genotypic data files.import_vcf: Provides support for importing VCF (Variant Call Format) data files.plot_SNP: Visualizes SNP distribution on a chromosome map.plot_summariseSNP: Plots SNP distribution across chromosomes.summariseSNP: Calculates SNP distribution across chromosomes.summariseSNP_vcf: Calculates SNP distribution across chromosomes from VCF data.
Sample Data Additions
sample_data_rice, sample_data_rice_qtl: Added rice sample datasets.sample_data_wheat, sample_data_wheat_custom, sample_data_wheat_qtl: Added wheat sample datasets.
Enhancements
- Improved functionality and performance of existing features.
- Updated documentation for better clarity and usability.