User: archie

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archie90
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India
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1 month, 3 weeks ago
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Posts by archie

<prev • 88 results • page 1 of 9 • next >
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include vcf header
... I used vscan2vcf.py to convert somatic text (from varscan) output to vcf output by software available at https://github.com/student-t/Varscan2VCF Input look like : chrom position ref var normal_reads1 normal_reads2 normal_var_freq normal_gt tumor_reads1 tumor_reads2 tumor_var_freq tumor_gt somat ...
varscan written 8 weeks ago by archie90
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TCGA data , filtration and normalization
... I downloaded data using TCGA2STAT across two omics profiles using following code. library(TCGA2STAT) seq <- getTCGA(disease="OV", data.type="RNASeq2") met <- getTCGA(disease="OV", data.type="Methylation", type="all") seq.met <- OMICSBind(dat1 = seq$dat, dat2 = met$dat) str(seq.met) 1) ...
omics tcga genomics normalization written 10 weeks ago by archie90
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TCGA array expression and rnaseq expression batch correction
... Hi everyone In one of the article mentioned " Before starting the PDAC data analysis we first checked for possible batch effect in different types of data using Mbatch ". (Mishra et al 2019) here different data types refers to methylation, expression. 2) I found another script where batch effect ...
rnaseq tcga expression written 6 months ago by archie90
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Multi samples (Normal and Tumor) somatic SNPs identification
... Hi everyone I have bam files of multiples normal and tumor samples. For the efficient SNPs prediction, Its recommended to have merged multi sample vcf file. These are steps I followed 1. Mapping of all T and N samples to get multi samples bam file ( Tumor 20 Bam files : Normal 20 Bam files) 2. ...
vcf gatk snp mutlisamplevcf whole-exom written 6 months ago by archie90
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multi sample vcf to data matrix
... Hi everyone I have almost 50 VCF files consisting of information of somatic and germline SNPs. I need to convert this data from vcf to matrix format as given below : sample1 samples2 Gene1 0 1 Gene2 1 0 Gene3 1 ...
vcf gatk snp written 6 months ago by archie90 • updated 6 months ago by ATpoint32k
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Comment: C: TCGA survival data classification
... Thanks alot Kevin. It helped alot. ...
written 6 months ago by archie90
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TCGA survival data classification
... Hello everyone, I am working on one of the Ovarian cancer TCGA clinical data . I would like to classify patients into two classes based on the survival. I took the column days to death (short : less than three years survival (365*3) and long : > 365*3 : greater than three year survival and cla ...
tcga survival written 7 months ago by archie90 • updated 7 months ago by Kevin Blighe56k
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Answer: A: Merging variant calls of whole exome and RNA-seq
... Hi , You can go through this paper https://github.com/aradenbaugh/radia where authors mentioned use of DNA and RNA snps but it is tumor specific. I hope , this can work for you. ...
written 12 months ago by archie90
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Answer: C: Error of Netics : Multi omics intergration tool
... It worked for me. I downloaded fdr function from https://brainder.org/2011/09/05/fdr-corrected-fdr-adjusted-p-values/ I missed this information earlier. Test run is working now. Thanks ...
written 12 months ago by archie90
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Error of Netics : Multi omics intergration tool
... Hello everyone, I am running Netics code to prioritize genes in my project. Basically, I am working on PDAC cancer . I have transcriptome and mutation data. I am trying to run 'NETICS' code available at https://github.com/cbg-ethz/netics. As a very first step, I am trying to run test data given ...
multi omics integration netics written 13 months ago by archie90 • updated 12 months ago by WouterDeCoster43k

Latest awards to archie

Popular Question 10 weeks ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 3 months ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 4 months ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 5 months ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 8 months ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 8 months ago, created a question with more than 1,000 views. For Markduplicates in RNASEQ
Popular Question 8 months ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 9 months ago, created a question with more than 1,000 views. For Error while running discoSNP
Popular Question 12 months ago, created a question with more than 1,000 views. For rRNA in human
Scholar 12 months ago, created an answer that has been accepted. For C: Error of Netics : Multi omics intergration tool
Popular Question 14 months ago, created a question with more than 1,000 views. For rRNA in human

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