User: archie

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archie60
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Posts by archie

<prev • 75 results • page 1 of 8 • next >
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cytoscape subnetwork from WGCNA based modules
... Hello I have identified modules linked to some traits of interest in our study. All modules were imported in cytoscape. As next step, I want to predict subnetwork using TieDie ( one of the cytoscape App). One of the network consist of 102 edges and 306 nodes. After running, TieDie on that netwo ...
tiedie subnetwork cytoscape written 6 days ago by archie60 • updated 5 days ago by Ram17k
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Comment: C: TCGA SNP data
... Hello My problem is during conversion from maf to vcf, loosing many SNP sites or data information via by use of maf2vcf.pl, which is not normal. I tried to fixed it, but not succeeded. Now I will follow your suggestion and will create custom PED and MAP. I already created .fam for dataset. Thank ...
written 6 weeks ago by archie60
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Comment: C: TCGA SNP data
... Dear kevin In one of project , converted vcf to plink and performed downstream analysis. Therefore I thought of following the same strategy for TCGA as well . For "custom PED and MAP", ya i will check. Thanks for your suggestion Archana ...
written 6 weeks ago by archie60
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TCGA SNP data
... Dear all In one of my project, I have to use the SNPs from TCGA (PAAD) and convert them into plink format and use for further analysis. There are many issues , that I faced 1. I was not able to capture all the sites while convering .maf to .vcf. Although I used exactly same genome version as men ...
maf2vcf snps paad tcga written 7 weeks ago by archie60 • updated 7 weeks ago by Kevin Blighe28k
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Comment: C: how to create .gzi index
... It worked using bgzip. :) ...
written 8 weeks ago by archie60
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how to create .gzi index
... Hello I am human reference genome in .gz format "Homo_sapiens.GRCh38.dna.toplevel.fa.gz" . I need to create its .gzi index to load reference genome. Can anyone guide me here? I will appreciate all suggestions Thank you in advance Archana ...
rnaseq genome written 8 weeks ago by archie60 • updated 8 weeks ago by harish130
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error while running vcf2maf
... Hi I have snps from rnaseq data. I split multisample file into single sample files. Now each sample vcf, I want to convert vcf to maf in vcf2maf . I am getting following error perl /usr/local/bin/vcf2maf.pl --input-vcf F545_altref_vep.vcf --output-maf F545_altref_vep.maf --tumor-id WD1309 ...
rnaseq vcf2maf snp written 8 weeks ago by archie60 • updated 8 weeks ago by h.mon19k
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Comment: C: Immunogenic signature in genesset
... Dear Kevin Thanks for this detail. I am not a bioloigst. Therefore it not easy for me to correlate results with hypothesis, I am working on. Thank you giving a clue here. :) Archana ...
written 8 weeks ago by archie60
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Immunogenic signature in genesset
... Hello everyone I want to predict immunogenic signatures in my gene list. I downloaded immunogenicsignature list from http://software.broadinstitute.org/gsea/msigdb/ and performed enrichment using my gene list. As a result, I am getting enrichment of some of the IDs with fdr 0.05 . IDs list is given ...
msigdb rnaseq immunogenic signatures written 8 weeks ago by archie60 • updated 8 weeks ago by Kevin Blighe28k
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Comment: C: upsetplot in clusterprofiler
... Hi Ram Upsetplot is supported in clusterprofiler as indicated in visulisation https://bioconductor.org/packages/release/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html. For me its not working. I tring to fix it. ...
written 9 weeks ago by archie60

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