arahuja/cufflinks-cibersort

Running a collection of cufflinks gene FPKM files through CIBERSORT

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cufflinks-cibersort

Running a collection of cufflinks gene FPKM files through CIBERSORT

Dependencies

  • R
  • Rserve for R
  • CIBERSORT jar

Running example

python 
    cufflinks-cibersort.py 
        --cufflinks-files cufflinks-all-samples/*/gene*fpkm* 
        --mixture-file CIBERSORT_package/LM22.txt 
        --cibersort-jar CIBERSORT_package/CIBERSORT.jar 
        --output cibersort-output.tsv 
        --print-top-n

Usage

python cufflinks-cibersort.py
usage: cufflinks-cibersort.py [-h] --cufflinks-files CUFFLINKS_FILES
                              [CUFFLINKS_FILES ...] [--gep-output GEP_OUTPUT]
                              --output OUTPUT
                              [--cibersort-output CIBERSORT_OUTPUT]
                              --mixture-file MIXTURE_FILE --cibersort-jar
                              CIBERSORT_JAR [--min-fpkm MIN_FPKM]
                              [--print-top-n] [--n N]
cufflinks-cibersort.py: error: the following arguments are required: --cufflinks-files, --output, --mixture-file, --cibersort-jar

Contributors

arahuja

Issues