# 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.
