• Well-defined subtypes of cancers in TCGA database

    I need data for some cancers which include well-defined subtypes/groups and be available in TCGA....

  • Is the PAM50 subtype available for TCGA BRCA data?

    I have some UNC Illumina RNAseqV2 data with about 100 genes, 800 patients with UNC ID. I'd like t...

  • Are there any tools that can extract somatic variants from matched normal tumor vcf files?

    Hello all, I have a set of VCF files of normal and tumor samples. Are there any tools available t...

  • TCGA RNAseq normal and tumor samples problem

    Hi,

    First of all, I want to clarify that I dont think TCGA can do RNA seq only for tumor sample?...

  • Method to classify given sample into subtype

    Hello,

    I am doing a small assignment for an intro to computational biology class, and I was told...

  • Normal sample variant calling method without PON ?

    Good day,

    I'm trying to recreate pipeline that was described in [Bioinformatics Analysis of Whol...

  • How many non-tumor samples needed for survival analysis?

    Hi All,
    I've been working on my own survival analysis of PDAC, following the tutorial ww...

  • Differential expression analysis error - TCGAbiolinks

    Hi Everyone,

    I am trying to analyze TCGA-BRCA (harmonized) data using TCGAbiolinks and I am stuc...

  • Tumor subtype: nearest centroid classifier

    I have a signature genes similar to pam50 (breast cancer signature) from other tumor. How should ...

  • Matched paired DEA analysis of BRCA samples using TCGAbiolinks, works for paired = FALSE but not paired = TRUE

    I am attempting to do a DEA analysis of matched paired BRCA normal tumour samples using TCGAbioli...

  • what does rsem.genesnormalised_result files in tcga database suggest

    I have downloaded BRCA patient data from TCGA. There is rsem.genes.normalised_result file associa...

  • Can PAM50 classification performed on TCGA-BRCA RNASeq RSEM data be used with RNASeq FPKM normalized data for downstream analysis?

    Hi Everyone,

    I was provided with TCGA-BRCA RNASeq V2 FPKM Tumor-Normal matched data which I inte...

  • How to perform a specific Coxph analysis using a continuous variable?

    Hello - I am new to survival analysis and would like to perform category specific Coxph analysis ...

  • False positives in manta structural variant calling

    Hi guys,

    I'm analyzing **structural variants** in paired tumor-healthy human samples with **[man...



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