User: Didi

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Didi10
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1 month ago
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3 years, 2 months ago
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Posts by Didi

<prev • 33 results • page 1 of 4 • next >
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Comment: C: external_gene_id attribute removed from new biomaRt version
... Hi, I'm using : library("biomaRt") ensembl <- useMart(biomart = "plants_mart", dataset = "athaliana_eg_gene", host = "plants.ensembl.org") features <- getBM(attributes = c("ensembl_gene_id", ...
written 4 weeks ago by Didi10
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external_gene_id attribute removed from new biomaRt version
... Hi, I couldn't find the external_gene_id attribute in the new biomaRt version. Is there any reason for that? Thanks a lot. D. ...
biomart ensembl ensemblplants written 4 weeks ago by Didi10
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Comment: C: how to run old scripts using corresponding biomaRt versions from archives
... Thanks a lot for your answer. I have this script from 2016. library(biomaRt) mart = useEnsembl(biomart="plants_mart", host="plants.ensembl.org", dataset = "osativa_eg_gene") bm <- useMart(host = "plants.ensembl.org", biomart="plants_mart", dataset = "osativa_eg_gene") I ...
written 5 weeks ago by Didi10
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how to run old scripts using corresponding biomaRt versions from archives
... Hi, Is there a way I can check the archive versions of bioamRt and then use one them to run. I have an old scripts from 2016, 2017 and 2018 and I want to rerun them with their corresponding version of biomaRt. Thanks a lot. D. ...
biomart bioconductor written 5 weeks ago by Didi10 • updated 5 weeks ago by Mike Smith3.8k
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biomaRt error message
... Hi, I downloaded the latest version of biomaRt and tried to run: m1 <- useMart("plants_mart", "osativa_eg_gene", host = "archive.plants.ensembl.org") go <- getBM(attributes=c("go_accession", "tigr_locus", "entrezgene","go_namespace_1003"),mart=m1) Since the "tigr_locus" attribute name chang ...
biomart bioconductor rice written 9 months ago by Didi10
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Comment: C: GEOquery using keywords in R
... I don't know if it's possible instead of using GSE accession numbers to use keywords like c("arabidopsis", "drought") and get all the related GSE accesion numbers. Is there any way to do that? ...
written 14 months ago by Didi10
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GEOquery using keywords in R
... Hi, How to do a GEO query using keywords in R? I found a few publications but they use the GSE accession number: GEO_DATASETS <- c("GSE73835") eset <- getGEOdataObjects(GEO_DATASETS[1]) eset   Thanks a lot. D. ...
geoquery geometadb geo written 14 months ago by Didi10 • updated 14 months ago by Sean Davis21k
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Comment: C: error when using ensembldb with a MySQL server
... Thanks a lot. ...
written 19 months ago by Didi10
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Comment: C: error when using ensembldb with a MySQL server
... Thanks a lot. When using  mysql -h localhost -u readonly -p I'm getting this error: ERROR 1045 (28000): Access denied for user 'readonly'@'localhost' (using password: YES)   ...
written 19 months ago by Didi10
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error when using ensembldb with a MySQL server
... Hi,  When trying to run this script through R, I've got the error highlighted in yellow. Any idea how to solve this issue? Thanks a lot. Cheers, Didi > library(ensembldb) > library(RMySQL) > dbcon <- dbConnect(MySQL(), host = "localhost", user = "readonly", + ...
rmysql ensembldb written 19 months ago by Didi10 • updated 19 months ago by James W. MacDonald50k

Latest awards to Didi

Popular Question 4 weeks ago, created a question with more than 1,000 views. For VariantAnnotation: Error with ScanVcfParam
Popular Question 8 months ago, created a question with more than 1,000 views. For Getting errors with makeTxDbFromBiomart

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