Question: Retrieve tissue expression in Zfin (R/python)
0
gravatar for A. Domingues
4.0 years ago by
A. Domingues2.2k
Dresden, Germany
A. Domingues2.2k wrote:

In zfin it is possible to find in which tissue/developmental stage a gene is expressed. The question is:

Is there a way of querying the database for this information using R/Python/bash? 

I naively assumed that someone would have added that information as a bioconductor package. but could not find it. 

zfin zebrafish latest danio rerio • 1.1k views
ADD COMMENTlink modified 3.4 years ago by julien.roux100 • written 4.0 years ago by A. Domingues2.2k

Hi. I'm also interested in this. Did you find a way to retrieve tissue expression in Zfin? thanks

ADD REPLYlink written 3.4 years ago by teresa.noviello890
3
gravatar for julien.roux
3.4 years ago by
julien.roux100
Switzerland
julien.roux100 wrote:

We have integrated in situ hybridization data from ZFIN in the Bgee database (http://bgee.org/). You can download the expression calls as flat files, but please have a look at the BgeeDB Bioconductor package as well (http://bioconductor.org/packages/release/bioc/html/BgeeDB.html), since you can download these calls directly into R:

source("https://bioconductor.org/biocLite.R")
biocLite("BgeeDB")
library(BgeeDB)
myTopAnatData <- loadTopAnatData(species=7955, datatype="in_situ")
head(myTopAnatData$gene2anatomy)

Please note, that we also provide expression calls for many other animal species and from other data types (RNA-seq, Affymetrix microarrays and ESTs) Please do not hesitate to contact the Bgee team if you need more help: bgee -at- sib.swiss

ADD COMMENTlink written 3.4 years ago by julien.roux100

Cheers. I will test this (in a few weeks time), and report back.

ADD REPLYlink written 3.4 years ago by A. Domingues2.2k
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