geneNR 3.0.0

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

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.