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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.sample_crop.gff3) that
automatically handles coordinate mapping when local mode is selected
without a file path, ensuring out-of-the-box functionality.geneSNP(),
geneQTL(), and geneSNPcustom(). The package
now safely balances real-time web-scraping from Ensembl Plants and
ultra-fast local coordinate intersections.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_rice,
sample_data_rice_qtl: Added rice sample
datasets.sample_data_wheat,
sample_data_wheat_custom,
sample_data_wheat_qtl: Added wheat sample
datasets.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.