Tag: GDAC

DESeq2 input from GDAC firehose

Hi guys, I hope you are fine. I’m not good in English so if you couldn’t understand my question, please feel free to reply. I’m a beginner of bioinformatics. I want to practice differential expressed gene (DEG) analysis in R. The RNA seq data I used was downloaded from broad…

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Bioconductor – RTCGA.mRNA

DOI: 10.18129/B9.bioc.RTCGA.mRNA     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see RTCGA.mRNA. mRNA datasets from The Cancer Genome Atlas Project Bioconductor version: 3.11 Package provides mRNA datasets from The Cancer Genome Atlas Project for all available cohorts types from gdac.broadinstitute.org/. Data format…

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TCGA survival by gene expression. Gene is missing everywhere I look, but should be possible?

TCGA survival by gene expression. Gene is missing everywhere I look, but should be possible? 0 Hello, I am trying to generate TCGA survival plots with gene expression data. I found a few interesting guides out there, but the genes I am interested in don’t work. The genes I want…

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Bioconductor – RTCGA.rnaseq

DOI: 10.18129/B9.bioc.RTCGA.rnaseq     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see RTCGA.rnaseq. Rna-seq datasets from The Cancer Genome Atlas Project Bioconductor version: 3.10 Package provides rna-seq datasets from The Cancer Genome Atlas Project for all cohorts types from gdac.broadinstitute.org/. Rna-seq data format…

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regarding coexpression analysis (by pearson method) of genes shortlisted from expression profile of a dataset obtained from GDAC Firehouse database

regarding coexpression analysis (by pearson method) of genes shortlisted from expression profile of a dataset obtained from GDAC Firehouse database 0 Hello guys, Should i consider genes having “zero” normalized count given in expression data of a dataset while doing coexpression analysis with respect to a particular gene (whose expression…

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