Tag: recount2

low / high grade ovarian cancer

TCGA data: low / high grade ovarian cancer 0 Dear All, I have downloaded ovarian cancer annotation data from the TCGA using the TCGAbiolinks package (recount2 data) as follows: ovary_rec2_gtex <- TCGAquery_recount2(project=”gtex”, tissue = “ovary”) tcga_sampleAnnot <- data.frame(ovary_rec2_tcga_scaled@colData) I can check the cancer type with command like this one unique(tcga_sampleAnnotgdc_cases.project.name)…

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Differential expression analysis between normal/cancer on recount2 data

Differential expression analysis between normal/cancer on recount2 data 0 Hi everyone, I have download GTEX data and TCGA data (only tumor samples available) for a given cancer type using the “recount” R package. After having filtered the genes that are in common between the 2 datasets, I would like to…

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