Supported by Dr. Osamu Ogasawara and  providing  . |
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Last data update: 2014.03.03 |
Supported OrganismsDescriptionLists which genomes and gene ids are supported for gene lengths and for gene ontology UsagesupportedOrganisms() DetailsGoseq allows a user to provide their own bias data (usually gene lengths) and/or gene categories (usually gene ontologies),
but goseq also provides this data automatically for many commonly used species. This function lists which genome and gene ids
are automatically supported by goseq. The first to third columns list the genomes, gene ids, and gene id descriptions
respectively. The fourth column indicates whether this combination of genome and id are available in the geneLengthDataBase.
If a particular combination is absent, goseq may still automatically fetch the gene lengths from either a TxDB annotation
package (must be installed) or download the data from UCSC. For example gene lengths for ValueA data.frame containing supported genomes and gene ids Author(s)Nadia Davidson nadia.davidson@mcri.edu.au ExamplessupportedOrganisms() Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(goseq)
Loading required package: BiasedUrn
Loading required package: geneLenDataBase
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/goseq/supportedOrganisms.Rd_%03d_medium.png", width=480, height=480)
> ### Name: supportedOrganisms
> ### Title: Supported Organisms
> ### Aliases: supportedOrganisms
>
> ### ** Examples
>
> supportedOrganisms()
Loading required package: rtracklayer
Loading required package: GenomicRanges
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: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Genome Id Id Description Lengths in geneLeneDataBase
12 anoCar1 ensGene Ensembl gene ID TRUE
13 anoGam1 ensGene Ensembl gene ID TRUE
14 apiMel2 ensGene Ensembl gene ID TRUE
56 bosTau2 geneSymbol Gene Symbol TRUE
15 bosTau3 ensGene Ensembl gene ID TRUE
57 bosTau3 geneSymbol Gene Symbol TRUE
16 bosTau4 ensGene Ensembl gene ID TRUE
58 bosTau4 geneSymbol Gene Symbol TRUE
17 canFam1 ensGene Ensembl gene ID TRUE
59 canFam1 geneSymbol Gene Symbol TRUE
18 canFam2 ensGene Ensembl gene ID TRUE
60 canFam2 geneSymbol Gene Symbol TRUE
19 cavPor3 ensGene Ensembl gene ID TRUE
61 ce2 geneSymbol Gene Symbol TRUE
62 ce4 geneSymbol Gene Symbol TRUE
20 ce6 ensGene Ensembl gene ID TRUE
63 ce6 geneSymbol Gene Symbol TRUE
64 ci1 geneSymbol Gene Symbol TRUE
21 ci2 ensGene Ensembl gene ID TRUE
65 ci2 geneSymbol Gene Symbol TRUE
22 danRer3 ensGene Ensembl gene ID TRUE
66 danRer3 geneSymbol Gene Symbol TRUE
23 danRer4 ensGene Ensembl gene ID TRUE
67 danRer4 geneSymbol Gene Symbol TRUE
10 danRer5 vegaGene HAVANA Pseudogene ID TRUE
24 danRer5 ensGene Ensembl gene ID TRUE
68 danRer5 geneSymbol Gene Symbol TRUE
25 danRer6 ensGene Ensembl gene ID TRUE
69 danRer6 geneSymbol Gene Symbol TRUE
70 dm1 geneSymbol Gene Symbol TRUE
71 dm2 geneSymbol Gene Symbol TRUE
72 dm3 geneSymbol Gene Symbol TRUE
73 equCab1 geneSymbol Gene Symbol TRUE
26 equCab2 ensGene Ensembl gene ID TRUE
74 equCab2 geneSymbol Gene Symbol TRUE
27 felCat3 ensGene Ensembl gene ID TRUE
75 felCat3 geneSymbol Gene Symbol TRUE
28 fr1 ensGene Ensembl gene ID TRUE
29 fr2 ensGene Ensembl gene ID TRUE
30 galGal2 ensGene Ensembl gene ID TRUE
76 galGal2 geneSymbol Gene Symbol TRUE
31 galGal3 ensGene Ensembl gene ID TRUE
77 galGal3 geneSymbol Gene Symbol TRUE
32 gasAcu1 ensGene Ensembl gene ID TRUE
1 hg16 knownGene Entrez Gene ID TRUE
33 hg16 ensGene Ensembl gene ID TRUE
78 hg16 geneSymbol Gene Symbol TRUE
2 hg17 knownGene Entrez Gene ID TRUE
11 hg17 vegaGene HAVANA Pseudogene ID TRUE
34 hg17 ensGene Ensembl gene ID TRUE
79 hg17 geneSymbol Gene Symbol TRUE
3 hg18 knownGene Entrez Gene ID TRUE
35 hg18 ensGene Ensembl gene ID TRUE
80 hg18 geneSymbol Gene Symbol TRUE
4 hg19 knownGene Entrez Gene ID TRUE
36 hg19 ensGene Ensembl gene ID TRUE
81 hg19 geneSymbol Gene Symbol TRUE
5 mm7 knownGene Entrez Gene ID TRUE
37 mm7 ensGene Ensembl gene ID TRUE
82 mm7 geneSymbol Gene Symbol TRUE
6 mm8 knownGene Entrez Gene ID TRUE
38 mm8 ensGene Ensembl gene ID TRUE
83 mm8 geneSymbol Gene Symbol TRUE
7 mm9 knownGene Entrez Gene ID TRUE
39 mm9 ensGene Ensembl gene ID TRUE
84 mm9 geneSymbol Gene Symbol TRUE
40 monDom4 ensGene Ensembl gene ID TRUE
85 monDom4 geneSymbol Gene Symbol TRUE
41 monDom5 ensGene Ensembl gene ID TRUE
86 monDom5 geneSymbol Gene Symbol TRUE
42 ornAna1 ensGene Ensembl gene ID TRUE
87 ornAna1 geneSymbol Gene Symbol TRUE
43 oryLat2 ensGene Ensembl gene ID TRUE
88 oryLat2 geneSymbol Gene Symbol TRUE
44 panTro1 ensGene Ensembl gene ID TRUE
45 panTro2 ensGene Ensembl gene ID TRUE
89 panTro2 geneSymbol Gene Symbol TRUE
46 ponAbe2 ensGene Ensembl gene ID TRUE
90 ponAbe2 geneSymbol Gene Symbol TRUE
47 rheMac2 ensGene Ensembl gene ID TRUE
91 rheMac2 geneSymbol Gene Symbol TRUE
8 rn3 knownGene Entrez Gene ID TRUE
48 rn3 ensGene Ensembl gene ID TRUE
92 rn3 geneSymbol Gene Symbol TRUE
9 rn4 knownGene Entrez Gene ID TRUE
49 rn4 ensGene Ensembl gene ID TRUE
93 rn4 geneSymbol Gene Symbol TRUE
50 sacCer1 ensGene Ensembl gene ID TRUE
51 sacCer2 ensGene Ensembl gene ID TRUE
94 strPur1 geneSymbol Gene Symbol TRUE
95 strPur2 geneSymbol Gene Symbol TRUE
52 taeGut1 ensGene Ensembl gene ID TRUE
96 taeGut1 geneSymbol Gene Symbol TRUE
53 tetNig1 ensGene Ensembl gene ID TRUE
54 tetNig2 ensGene Ensembl gene ID TRUE
55 xenTro2 ensGene Ensembl gene ID TRUE
97 xenTro2 geneSymbol Gene Symbol TRUE
122 Arabidopsis FALSE
123 E. coli K12 FALSE
124 E. coli Sakai FALSE
125 Malaria FALSE
103 bosTau6 FALSE
102 bosTau7 FALSE
101 bosTau8 FALSE
104 canFam3 FALSE
120 ce10 FALSE
119 ce11 FALSE
116 danRer10 FALSE
117 danRer7 FALSE
118 dm6 FALSE
112 galGal4 FALSE
98 hg38 FALSE
105 mm10 FALSE
100 panTro3 FALSE
99 panTro4 FALSE
111 rheMac3 FALSE
110 rheMac8 FALSE
109 rn5 FALSE
108 rn6 FALSE
121 sacCer3 FALSE
107 susScr2 FALSE
106 susScr3 FALSE
115 xenTro1 FALSE
114 xenTro3 FALSE
113 xenTro7 FALSE
GO Annotation Available
12 FALSE
13 TRUE
14 FALSE
56 TRUE
15 TRUE
57 TRUE
16 TRUE
58 TRUE
17 TRUE
59 TRUE
18 TRUE
60 TRUE
19 FALSE
61 TRUE
62 TRUE
20 TRUE
63 TRUE
64 FALSE
21 FALSE
65 FALSE
22 TRUE
66 TRUE
23 TRUE
67 TRUE
10 FALSE
24 TRUE
68 TRUE
25 TRUE
69 TRUE
70 TRUE
71 TRUE
72 TRUE
73 FALSE
26 FALSE
74 FALSE
27 FALSE
75 FALSE
28 FALSE
29 FALSE
30 TRUE
76 TRUE
31 TRUE
77 TRUE
32 FALSE
1 TRUE
33 TRUE
78 TRUE
2 TRUE
11 FALSE
34 TRUE
79 TRUE
3 TRUE
35 TRUE
80 TRUE
4 TRUE
36 TRUE
81 TRUE
5 TRUE
37 TRUE
82 TRUE
6 TRUE
38 TRUE
83 TRUE
7 TRUE
39 TRUE
84 TRUE
40 FALSE
85 FALSE
41 FALSE
86 FALSE
42 FALSE
87 FALSE
43 FALSE
88 FALSE
44 TRUE
45 TRUE
89 TRUE
46 FALSE
90 FALSE
47 TRUE
91 TRUE
8 TRUE
48 TRUE
92 TRUE
9 TRUE
49 TRUE
93 TRUE
50 TRUE
51 TRUE
94 FALSE
95 FALSE
52 FALSE
96 FALSE
53 FALSE
54 FALSE
55 TRUE
97 TRUE
122 TRUE
123 TRUE
124 TRUE
125 TRUE
103 TRUE
102 TRUE
101 TRUE
104 TRUE
120 TRUE
119 TRUE
116 TRUE
117 TRUE
118 TRUE
112 TRUE
98 TRUE
105 TRUE
100 TRUE
99 TRUE
111 TRUE
110 TRUE
109 TRUE
108 TRUE
121 TRUE
107 TRUE
106 TRUE
115 TRUE
114 TRUE
113 TRUE
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> dev.off()
null device
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Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and