User: thind.amarinder

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20
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New User
Location:
Italy
Last seen:
19 hours ago
Joined:
5 years, 1 month ago
Email:
t**************@gmail.com

Posts by thind.amarinder

<prev • 25 results • page 1 of 3 • next >
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Comment: C: How to convert maf file format to oncoPrint matrix (ComplexHeatmap package)?
... Thanks for sharing. However, I already did that. Following is the outline of the code colnames(data2) <- c("Samples","Gene","Impact") ### remove duplicate rows data <-data[!duplicated(data[,]),] for(i in 1:nrow(data)) { for(j in 1:nrow(data)) { if(i ...
written 7 days ago by thind.amarinder20
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Comment: C: Conversion of Vep.vcf to MAF format?
... I am trying, they wrote If you already annotated a VCF with either VEP or snpEff, you can use those directly: perl vcf2maf.pl --input-vep test.vep.vcf --output-maf test.maf perl vcf2maf.pl --input-snpeff test.snpeff.vcf --output-maf test.maf ...
written 7 days ago by thind.amarinder20
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Answer: A: Conversion of Vep.vcf to MAF format?
... I got my answer. It is possible with https://github.com/mskcc/vcf2maf/releases/tag/v1.1.0 ...
written 7 days ago by thind.amarinder20
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Comment: C: Conversion of Vep.vcf to MAF format?
... not really, I have annotated vcf by VEP. not .vcf ...
written 7 days ago by thind.amarinder20
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Comment: C: How to compare and visualize own data with other cBioportal based studies?
... Thanks, cBioportal informed me that I have to make my data public for using the online version. So maybe I should explore, how I can use download and data of other studies in the local version. I am not sure, if it is possible. ...
written 14 days ago by thind.amarinder20
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Comment: C: How to compare and visualize own data with other cBioportal based studies?
... Thanks for your valuable reply. I am wondering, using the local cBioportal If, I can use data from other studies available at online version? ...
written 14 days ago by thind.amarinder20
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Comment: C: How to compare and visualize own data with other cBioportal based studies?
... It is Mutations and cnv data. I am mainly interested in Oncoprint . ...
written 14 days ago by thind.amarinder20
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How to compare and visualize own data with other cBioportal based studies?
... How I can compare my own data with data available in cBioportal and make oncoprint from combined studies. I don't want to make my data public at the moment. ...
tcga cbioportal written 14 days ago by thind.amarinder20 • updated 14 days ago by genomax84k
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Conversion of Vep.vcf to MAF format?
... I have Vep.vcf files and I would like to convert it into MAF. But I do not want to execute VEP again, as required by vcf2maf. What are the other possibilities? ...
maf genome vep snp cancer written 14 days ago by thind.amarinder20
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Comment: C: vcf2maf VEP annotated VCF conversion
... @martina I was wondering if you have solved the problem. I have vep.vcf file and want to convert it into MAF. ...
written 16 days ago by thind.amarinder20

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