Running a collection of cufflinks gene FPKM files through CIBERSORT
- R
Rservefor R- CIBERSORT jar
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-npython cufflinks-cibersort.pyusage: 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