User: Didi

gravatar for Didi
Didi10
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10
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New User
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2 months, 3 weeks ago
Joined:
3 years, 6 months ago
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h*********@hotmail.com

Posts by Didi

<prev • 33 results • page 2 of 4 • next >
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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 2.3 years ago by Didi10
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Comment: C: VariantAnnotation: Error with ScanVcfParam
... It's working.  Thanks a lot.   ...
written 2.4 years 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 2.4 years 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 2.4 years ago by Didi10
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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 2.4 years ago by Didi10
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add annotation features to BSgenome or txdb package
... Hi,  Is it possible to add annotation features to a BSgenome package or a txdb package in case there isn't an orgDB package for non model organisms? Is it easy to do it? Thanks a lot.  Regards, D. ...
annotation bsgenome orgdb txdb written 2.4 years ago by Didi10
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Answer: A: Cytoband information for rice
... Thanks a lot.  Regards, D.   ...
written 2.4 years ago by Didi10
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Cytoband information for rice
... Hi, Does anyone know from where getting the cytoband information for rice (Oryza sativa) to draw the ideogram for a circular visualization? Thanks a lot. Regards, D. ...
ideogram ggbio rice cytoband circlize written 2.4 years ago by Didi10
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Answer: A: BiomaRt package not working
... Thank you so much. It's working now by using : go <- getBM(attributes = c("go_id", "tair_locus", "namespace_1003"),              mart=ensembl) It was really helpful. Thanks again.   ...
written 2.6 years ago by Didi10
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Comment: C: BiomaRt package not working
... Thanks a lot.  ...
written 2.6 years ago by Didi10

Latest awards to Didi

Popular Question 5 months ago, created a question with more than 1,000 views. For VariantAnnotation: Error with ScanVcfParam
Popular Question 12 months ago, created a question with more than 1,000 views. For Getting errors with makeTxDbFromBiomart

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