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Update analyses/immune-deconv/run-immune-deconv.sh
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Co-Authored-By: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
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@komalsrathi @jaclyn-taroni
komalsrathi and jaclyn-taroni authored Jan 3, 2020
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Expand Up @@ -18,7 +18,7 @@ cd "$script_directory" || exit

# create results directory if it doesn't already exist
mkdir -p results

mkdir -p plots
# generate deconvolution output for poly-A and stranded datasets using xCell and the second specified method
# we will use CIBERSORT for the paper but because the dependent scripts are not publicly accesible, we will use the next best method i.e. MCP-counter as default for testing purpose
# Reference for benchmarking between xCell, CIBERSORT and MCP-counter: PMID: 31641033
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