Question

biomarRt for fungi

1

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sunjae.lee ▴ 20

@sunjaelee-19370

Last seen 5.3 years ago

Hello Everyone!

is there anyone knows how I can access fungal information from biomaRt?

I once saw Ensembl fungi was in there, but now I couldn't find it.

any clues will be a great help to me.

Thank you for your time on this question.

Best

Sunjae

biomaRt • 1.6k views

ADD COMMENT • link updated 5.3 years ago by Mike Smith ★ 6.5k • written 5.3 years ago by sunjae.lee ▴ 20

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Dear Sunjae,

I am afraid that we are experiencing issues with our Fungi marts at the moment. I will let you know once the our service is back to normal.

Apologies for any inconvenience caused. Kind Regards, Thomas

ADD REPLY • link 5.3 years ago Thomas Maurel ▴ 800

score 3 · Answer 1 · 2019-01-11

You should still be able to access the Ensembl Fungi data using biomaRt. Does this work for you?

library(biomaRt)
ensembl_fungi <- useMart(host="https://fungi.ensembl.org", 
                         biomart="fungi_mart", 
                         port = 443)
head(listDatasets(ensembl_fungi))

                  dataset                                        description        version
1       aclavatus_eg_gene       Aspergillus clavatus NRRL 1 genes (ASM271v1)       ASM271v1
2         aflavus_eg_gene Aspergillus flavus NRRL3357 genes (JCVI-afl1-v2.0) JCVI-afl1-v2.0
3      afumigatus_eg_gene       Aspergillus fumigatus Af293 genes (ASM265v1)       ASM265v1
4 afumigatusa1163_eg_gene     Aspergillus fumigatus A1163 genes (ASM15014v1)     ASM15014v1
5       agossypii_eg_gene                  Ashbya gossypii genes (ASM9102v1)      ASM9102v1
6       anidulans_eg_gene     Aspergillus nidulans FGSC A4 genes (ASM1142v1)      ASM1142v1