User: Didi

gravatar for Didi
Didi10
Reputation:
10
Status:
New User
Location:
Last seen:
1 week, 1 day ago
Joined:
2 years, 4 months ago
Email:
h*********@hotmail.com

Posts by Didi

<prev • 28 results • page 1 of 3 • next >
0
votes
1
answers
117
views
1
answers
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 4 months ago by Didi10
0
votes
1
answer
117
views
1
answer
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 4 months ago by Didi10 • updated 4 months ago by Sean Davis21k
0
votes
1
answers
350
views
1
answers
Comment: C: error when using ensembldb with a MySQL server
... Thanks a lot. ...
written 9 months ago by Didi10
0
votes
1
answers
350
views
1
answers
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 9 months ago by Didi10
0
votes
1
answer
350
views
1
answer
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 9 months ago by Didi10 • updated 9 months ago by James W. MacDonald48k
0
votes
0
answers
207
views
0
answers
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 13 months ago by Didi10
0
votes
1
answers
722
views
1
answers
Comment: C: VariantAnnotation: Error with ScanVcfParam
... It's working.  Thanks a lot.   ...
written 14 months ago by Didi10
0
votes
1
answers
722
views
1
answers
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 14 months ago by Didi10
2
votes
1
answer
722
views
1
answer
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 14 months ago by Didi10
0
votes
2
answers
764
views
2
answers
Answer: A: add annotation features to BSgenome or txdb package
... I have GTF and GFF files. I imported them as a TxDb object and it works. Thanks a lot. Regards, D. ...
written 14 months ago by Didi10

Latest awards to Didi

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 211 users visited in the last hour