.gitignore
.travis.yml
LICENSE.md
MANIFEST.in
README.md
conftest.py
requirements.txt
setup.py
sjaracne_workflow.yml
version.py
SJARACNe/Makefile
SJARACNe/__init__.py
SJARACNe/sjaracne.py
SJARACNe.egg-info/PKG-INFO
SJARACNe.egg-info/SOURCES.txt
SJARACNe.egg-info/dependency_links.txt
SJARACNe.egg-info/entry_points.txt
SJARACNe.egg-info/requires.txt
SJARACNe.egg-info/top_level.txt
SJARACNe/bin/QC_input.py
SJARACNe/bin/__init__.py
SJARACNe/bin/ch_line_ending.py
SJARACNe/bin/create_consensus_network.py
SJARACNe/bin/sjaracne.exe
SJARACNe/config/config_cwlexec.json
SJARACNe/config/config_kernel.txt
SJARACNe/config/config_threshold.txt
SJARACNe/cwl/QC_input.cwl
SJARACNe/cwl/ch_line_ending.cwl
SJARACNe/cwl/copy_files_to_dir.cwl
SJARACNe/cwl/create_consensus_network.cwl
SJARACNe/cwl/get_consensus_network.cwl
SJARACNe/cwl/get_enhanced_consensus_network.cwl
SJARACNe/cwl/int_to_int_array.cwl
SJARACNe/cwl/int_to_str_array.cwl
SJARACNe/cwl/sjaracne.cwl
SJARACNe/cwl/sjaracne_workflow.cwl
SJARACNe/src/main.cpp
SJARACNe/src/matrix.cpp
SJARACNe/src/matrix.h
SJARACNe/src/param.cpp
SJARACNe/src/param.h
SJARACNe/src/parseargs.h
SJARACNe/src/util.cpp
SJARACNe/src/util.h
test_data/inputs/BRCA100.exp
test_data/inputs/sig.txt
test_data/inputs/tf.txt
test_data/inputs/cwl/ch_line_ending.yml
test_data/inputs/cwl/copy_files_to_dir.yml
test_data/inputs/cwl/create_consensus_network.yml
test_data/inputs/cwl/intake_config.txt
test_data/inputs/cwl/intake_config.txt.bak
test_data/inputs/cwl/sjaracne.yml
test_data/inputs/cwl/sjaracne_workflow.yml
test_data/inputs/cwl/sub_gene_symbols.txt
test_data/outputs/cwl/intake_config_new.txt
test_data/outputs/cwl/cwltool/SJARACNE_out.final/sjaracne_workflow.yml
tests/sjaracne_workflow.yml
tests/test_ch_line_ending.py
tests/test_copy_files_to_dir.bats
tests/test_create_consensus_network.py
tests/test_int_to_int_array.bats
tests/test_int_to_str_array.bats
tests/test_sjaracne_acceptance.py
tests/test_sjaracne_lsf_brca_data.sh
tests/test_sjaracne_lsf_real_data.sh
tests/answerkey/bootstrap_info_.txt
tests/answerkey/consensus_network_3col_.txt
tests/answerkey/consensus_network_ncol_.txt
tests/answerkey/parameter_info_.txt
tests/answerkey/acceptance/bootstrap_info_.txt
tests/answerkey/acceptance/cnn_5.txt
tests/answerkey/acceptance/consensus_network_3col_.txt
tests/answerkey/acceptance/consensus_network_ncol_.txt
tests/answerkey/acceptance/parameter_info_.txt
tests/cwl/cwlexec/ch_line_ending.sh
tests/cwl/cwlexec/config.json
tests/cwl/cwlexec/create_consensus_network.sh
tests/cwl/cwlexec/sjaracne.sh
tests/cwl/cwlexec/sjaracne_workflow.sh
tests/cwl/cwltool/ch_line_ending.sh
tests/cwl/cwltool/create_consensus_network.sh
tests/cwl/cwltool/sjaracne.sh
tests/cwl/cwltool/sjaracne_workflow.sh
tests/inputs/BRCA100.exp
tests/inputs/Tcell1170.exp
tests/inputs/TcellTF.txt
tests/inputs/adjmat_dir/TF_run.adj
tests/logs/err.80957051.1.txt
tests/logs/out.80957051.1.txt
tests/logs/tracker_real.2019.06.17.err
tests/logs/tracker_real.2019.06.17.out