Match a species query to the regularized species info.
species_info(query = NULL, ...)a data.frame of species-related information that is used to fetch appropriate annotation files and conversion functions between species for gene identifiers, and such.
species_info()
#> alias species bioc_full bioc_abbrev kegg
#> 1 NA Ag aga
#> 2 NA At ath
#> 3 NA Bt bta
#> 4 worm Caenorhabditis elegans NA Ce cel
#> 5 fly Drosophila melanogaster NA Dm dme
#> 6 zebrafish Danio rerio NA Dr dre
#> 7 NA EcK12 eco
#> 8 NA EcSakai ecs
#> 9 NA Gg gga
#> 10 human Homo sapiens NA Hs hsa
#> 11 cyno Macaca fascicularis NA Mf mcf
#> 12 mouse Mus musculus NA Mm mmu
#> 13 rhesus Macaca mulatta NA Mmu mcc
#> 14 NA Pf pfa
#> 15 NA Pt ptr
#> 16 rat Rattus norvegicus NA Rn rno
#> 17 dog Canis lupus familiaris NA
#> 18 yeast Saccharomyces cerevisiae NA Ss ssc
#> 19 NA Xl xla
#> mart_dataset symbol_name
#> 1
#> 2
#> 3
#> 4
#> 5 flybasename_gene dmelanogaster_gene_ensembl
#> 6 drerio_gene_ensembl zfin_id_symbol
#> 7
#> 8
#> 9
#> 10 hsapiens_gene_ensembl hgnc_symbol
#> 11 mfascicularis_gene_ensembl external_gene_name
#> 12 mmusculus_gene_ensembl mgi_symbol
#> 13
#> 14
#> 15
#> 16
#> 17
#> 18
#> 19
species_info("human")
#> $alias
#> [1] "human"
#>
#> $species
#> [1] "Homo sapiens"
#>
#> $bioc_full
#> [1] NA
#>
#> $bioc_abbrev
#> [1] "Hs"
#>
#> $kegg
#> [1] "hsa"
#>
#> $mart_dataset
#> [1] "hsapiens_gene_ensembl"
#>
#> $symbol_name
#> [1] "hgnc_symbol"
#>