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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.
Health stats visible at Monitor.