A Pipeline to Define Gene Families in Legumes and Beyond

Documentation for package ‘geneHummus’ version 1.0.11

geneHummus-package	genehummus: A pipeline to define gene families in Legumes and beyond
accessions_by_spp	Compute the total number of accession proteins per species
accessions_from_spp	Extract the accession ids (XP accession) for a given organism
accessions_warning	Get acessions and organism for each protein identifier
archids_warning	Get architecture identifiers for the conserved domains
extract_proteins	Get the protein identifiers
filterarchids_warning	Filter protein architectures based on conserved domains
filterArch_ids	Filter the protein architectures based on conserved domains
geneHummus	genehummus: A pipeline to define gene families in Legumes and beyond
getAccessions	Get the acessions ids and the organism for each protein identifier
getArch_ids	Get the potential architecture identifiers for the conserved domains
getArch_labels	Get the description label for a protein architecture identifier
getProteins_from_tax_ids	Get the RefSeq protein identifiers for the given taxonomic species
getProtlinks	Get the protein identifiers for a given architecture
getSparcleArchs	Get the electronic architecture for a conserved domain
get_spp	Get the species name from the description sequence
labels_warning	Get description label for a protein architecture identifier
legumesIds	NCBI taxonomy ids for the legume family
my_legumes	ARF proteins per legume specie
proteins_warning	Get RefSeq protein identifiers for the given taxonomic species
sizeIds	Build a list containing N elements per element list