CPTAC RNA seq
Hey friends I am using python code to download CPTAC transcriptomic data. But this is not raw count data. my code is :
cptac.download(dataset="Ccrcc")
transcriptomics = en.get_transcriptomics()
transcriptomics.head()
transcriptomics.to_csv(path_or_buf="transcriptomics_dataframe.csv", sep=',')
How should I download the raw count transcriptomic?
thanks
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GDC has the count files openly available for CPTAC samples : https://portal.gdc.cancer.gov/repository?filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22CPTAC%22%5D%7D%2C%22op%22%3A%22in%22%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.access%22%2C%22value%22%3A%5B%22open%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.experimental_strategy%22%2C%22value%22%3A%5B%22RNA-Seq%22%5D%7D%7D%5D%7D