R: A Pipeline to Define Gene Families in Legumes and Beyond

# A Pipeline to Define Gene Families in Legumes and Beyond

## Documentation for package ‘geneHummus’ version 1.0.11

- DESCRIPTION file
- Package README

## Help Pages

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