User: archie

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archie50
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Posts by archie

<prev • 66 results • page 1 of 7 • next >
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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 1 day ago by archie50
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Comment: C: upsetplot in clusterprofiler
... Hi Thx for your reply . Here is my code , c1 <- read.table("c1.txt",header=T) c1g <- c1$c1 c1gg <- as.character(c1g) c1eg = bitr(c1gg, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Hs.eg.db") c2 <- read.table("c2.txt",header=T) c2g <- c2$c2 c2gg <- ...
written 1 day ago by archie50 • updated 1 day ago by Ram16k
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upsetplot in clusterprofiler
... Hi I have 6 groups and did the enrichKEGG and enrichGO in clusterprofiler and got comparative output in dotplot format. I want get the output in upsetplot format. How can I see the comparative output in upsetplot format? Thanks in advance Archana ...
R bioconductor clusterprofiler written 2 days ago by archie50 • updated 2 days ago by Guangchuang Yu1.9k
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Comment: C: TCGA SNP to plink
... Hi Here is Data link http://firebrowse.org/?cohort=PAAD I downloaded Mutation_Packager_Oncotated_Calls (MD5) under Mutation Annotation File. Thanks Archana ...
written 2 days ago by archie50
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TCGA SNP to plink
... Hello everyone I want to convert from TCGA SNP to PLINK. Can anyone suggest here 1. I downloaded MAF files from https://gdac.broadinstitute.org/ . Is it OK if I follow conversion MAF to VCF to PLINK ? 2. If yes, I worked on the conversion of MAF2VCF using maf2vcf.pl , but for every MAF file, I ...
maf tcga plink written 2 days ago by archie50
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Comment: C: How to get TCGA SNP in vcf and process in PLINK
... Hi First of all, defined the ref fasta my $ref_fasta = "/path/Homo_sapiens.GRCh37.75.dna.toplevel.fa" in script maf2vcf.pl and saved changes. Here is command used to convert maf to vcf . perl maf2vcf.pl --input-maf TCGA-IB-8127-01.maf.txt --output-dir TCGA-IB-8127-01.vcf Thank you in advan ...
written 3 days ago by archie50
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MatrixEpistasis input format
... Dear all, I have identified some SNPs from two groups of cancer. I want to analyse the SNP-SNP interaction. I have SNPs in vcf format. I have converted vcf to plink (.map and .ped) format. But while working on "A quick toy example",I found input is snp matrix with numeric data type. How to define t ...
matrixepistasis snp-snp interaction written 6 days ago by archie50
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Comment: C: How to get TCGA SNP in vcf and process in PLINK
... I checked respective position on given genome build, It was exactly same. Still I am getting this issue. Can anybody suggest me how to fix it ? Otherwise I will lose most of the SNPs information for downstream which I do not want to do. Or If its possible to create manual vcf ? How ? ...
written 7 days ago by archie50
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Comment: C: How to get TCGA SNP in vcf and process in PLINK
... Hi I did the same. During runtime of maf2vcf.pl I am getting warning WARNING: Reference allele mismatches found. Many of SNPs are getting filtered out . What should I do ? ...
written 7 days ago by archie50
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How to get TCGA SNP in vcf and process in PLINK
... Dear all I urgently want to download SNP information of TCGA-PAAD and run in PLINK for further analysis . I got the expression data of 183 samples. Is It possible to get SNPs of 183 samples in VCF ? waiting for reply All suggestions will be appreciated Thank you in advance Archana ...
vcf tcga plink written 7 days ago by archie50 • updated 7 days ago by pbpanigrahi170

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