npklein / decon-coreg

Deconvoluting cell type specific co-regulation from bulk samples

Decon-coreg is a modification of Decon-eQTL to allow interaction with gene expression instead of with SNPs

For compiling

commons-cli v1.3.1
commons-csv v1.2
commons-io v2.4
commons-lang3 v3.4
commons-math3 v3.6
jsci-core
jsci-mathmlimpl
jsci-sci

minimal usage example

java -jar Decon-coreg-v*.*.*-jar-with-dependencies.jar -c <file containing cellcounts> \
                        -e <file containing expression data> \
                        -o <output directory> \
                        -sn <file with gene gene combinations to test>

Options overview

-c,--cellcount <file>                     Cellcount file name
-e,--expression <file>                    Expression file name
-help                                     print this message
-no,--no_console                          Do not output logging info to the console
-o,--outfolder <path>                     Path to folder to write output to
-of,--outfile <file>                      Outfile name of deconvolution results (will be written in outfolder)
-sn,--genesToTest <file>                   Tab delimited file with first column gene name, second column gene name. files.
-t,--test_run                             Only run deconvolution for 100 QTLs for quick test run
-w,--whole_blood_qtl                      Add whole blood eQTL (pearson correlation genotypes and expression)