List species with Affymetrix or RNA-seq data in the Bgee database

Description

Returns a list of available genomes for different platforms in Bgee.

Usage

listBgeeSpecies(...)

Arguments

Value

A list of species with available Affymetrix or RNA-seq data in the Bgee

Author(s)

Andrea Komljenovic andrea.komljenovic at unil.ch.

Examples

{
 listBgeeSpecies()
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(BgeeDB)
Loading required package: topGO
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: graph
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums


Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

The following object is masked from 'package:IRanges':

    members

Loading required package: tidyr

Attaching package: 'tidyr'

The following object is masked from 'package:S4Vectors':

    expand

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/BgeeDB/listBgeeSpecies.Rd_%03d_medium.png", width=480, height=480)
> ### Name: listBgeeSpecies
> ### Title: List species with Affymetrix or RNA-seq data in the Bgee
> ###   database
> ### Aliases: listBgeeSpecies
> 
> ### ** Examples
> 
> {
+  listBgeeSpecies()
+ }
Last update: Jun2015 
$`Species in the Database`
      ID           GENUS      SPECIES     COMMON
1   9606            Homo      sapiens      human
2  10090             Mus     musculus      mouse
3   7955           Danio        rerio  zebrafish
4   7227      Drosophila melanogaster   fruitfly
5   6239  Caenorhabditis      elegans  c.elegans
6   9598             Pan  troglodytes chimpanzee
7   9597             Pan     paniscus     bonobo
8   9593         Gorilla      gorilla    gorilla
9   9544          Macaca      mulatta   macacque
10 10116          Rattus   norvegicus        rat
11  9913             Bos       taurus        cow
12  9823             Sus       scrofa        pig
13 13616     Monodelphis    domestica    opossum
14  9258 Ornithorhynchus     anatinus   platypus
15  9031          Gallus       gallus    chicken
16 28377          Anolis carolinensis     anolis
17  8364         Xenopus   tropicalis    xenopus
18  9600           Pongo     pygmaeus  orangutan
19 99883       Tetraodon nigroviridis  tetraodon

$RNAseq
 [1] "Anolis_carolinensis"      "Bos_taurus"              
 [3] "Caenorhabditis_elegans"   "Gallus_gallus"           
 [5] "Gorilla_gorilla"          "Homo_sapiens"            
 [7] "Macaca_mulatta"           "Monodelphis_domestica"   
 [9] "Mus_musculus"             "Ornithorhynchus_anatinus"
[11] "Pan_paniscus"             "Pan_troglodytes"         
[13] "Rattus_norvegicus"        "Sus_scrofa"              
[15] "Xenopus_tropicalis"      

$Affymetrix
[1] "Caenorhabditis_elegans"  "Danio_rerio"            
[3] "Drosophila_melanogaster" "Homo_sapiens"           
[5] "Mus_musculus"           

> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>