User: Didi

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Didi10
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1 week, 4 days ago
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2 years, 5 months ago
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Posts by Didi

<prev • 29 results • page 1 of 3 • next >
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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 4 weeks 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 6 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 6 months ago by Didi10 • updated 6 months ago by Sean Davis21k
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Comment: C: error when using ensembldb with a MySQL server
... Thanks a lot. ...
written 11 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 11 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 11 months ago by Didi10 • updated 11 months ago by James W. MacDonald48k
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Omiccircos: how to draw a circos plot for non-model organisms
... Hi, I was wondering how to draw a circos plot with cytoband data supplied by the user as a dataframe. In the documentation the segAnglePo and sim.circos functions use hg19/hg18 cytoband information from UCSC to form the anchor of the figure.  In case of  working with a non-model organism how to de ...
omiccircos seganglepo circos sim.circos written 15 months ago by Didi10
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Comment: C: VariantAnnotation: Error with ScanVcfParam
... It's working.  Thanks a lot.   ...
written 16 months ago by Didi10
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Comment: A: VariantAnnotation: Error with ScanVcfParam
... Hi, I checked and everything seems ok. headerTabix(tab)$seqnames [1] "Chr1" "Chr2" "Chr3" "Chr4" "Chr5" "Chr6" "Chr7" "Chr8" "Chr9" "Chr10" [11] "Chr11" "Chr12" I still don't know what's the problem. ...
written 16 months ago by Didi10
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VariantAnnotation: Error with ScanVcfParam
... Hi, I tried to get from the VCF file the SNPs that are in chr5 between 3-6Mb using this script and I've got this error. library(VariantAnnotation) library(Rsamtools) VARvcf <- readVcf("/media/Data/VAR_reads (Variants).vcf.gz") idx <- indexTabix("/media/Data/VAR_reads (Variants).vcf.gz", "vcf ...
variantannotation vcf readvcf filtervcf scanvcfparam written 16 months ago by Didi10

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