├── .gitignore ├── LICENSE ├── README.md ├── RUN_SICILIAN_post_process.sh ├── SICILIAN.png ├── SICILIAN.py ├── SICILIAN_post_process.py ├── benchmarking ├── README.md ├── ann_unann_scatter.py ├── benchmarking_files │ ├── Engstrom │ │ ├── sim1 │ │ │ └── GLM_output_benchmark_OL1.txt │ │ └── sim2 │ │ │ └── GLM_output_benchmark_OL1.txt │ └── HISAT │ │ ├── HISAT_mismatch │ │ └── GLM_output_benchmark_OL1.txt │ │ └── HISAT_perfect │ │ └── GLM_output_benchmark_OL1.txt ├── count_tables.py ├── figure_1E.R └── shared_concordance.py ├── requirements.txt └── scripts ├── GLM_script_light.R ├── Process_CI_10x.py ├── __pycache__ ├── annotator.cpython-36.pyc ├── annotator.cpython-37.pyc ├── light_utils.cpython-36.pyc ├── light_utils.cpython-37.pyc ├── utils_juncReads_minimal.cpython-36.pyc ├── utils_juncReads_minimal.cpython-37.pyc ├── utils_juncReads_minimal_HISAT.cpython-36.pyc ├── utils_os.cpython-36.pyc └── utils_os.cpython-37.pyc ├── ann_splices.py ├── annotator.py ├── annotator.pyc ├── consolidate_GLM_output_files.R ├── create_annotator.py ├── light_class_input.py ├── light_utils.py ├── post_processing.R ├── utils_os.py └── view_seqs.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/README.md -------------------------------------------------------------------------------- /RUN_SICILIAN_post_process.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/RUN_SICILIAN_post_process.sh -------------------------------------------------------------------------------- /SICILIAN.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/SICILIAN.png -------------------------------------------------------------------------------- /SICILIAN.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/SICILIAN.py -------------------------------------------------------------------------------- /SICILIAN_post_process.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/SICILIAN_post_process.py -------------------------------------------------------------------------------- /benchmarking/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/benchmarking/README.md -------------------------------------------------------------------------------- /benchmarking/ann_unann_scatter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/benchmarking/ann_unann_scatter.py -------------------------------------------------------------------------------- /benchmarking/benchmarking_files/Engstrom/sim1/GLM_output_benchmark_OL1.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/benchmarking/benchmarking_files/Engstrom/sim1/GLM_output_benchmark_OL1.txt -------------------------------------------------------------------------------- /benchmarking/benchmarking_files/Engstrom/sim2/GLM_output_benchmark_OL1.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/benchmarking/benchmarking_files/Engstrom/sim2/GLM_output_benchmark_OL1.txt -------------------------------------------------------------------------------- /benchmarking/benchmarking_files/HISAT/HISAT_mismatch/GLM_output_benchmark_OL1.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/benchmarking/benchmarking_files/HISAT/HISAT_mismatch/GLM_output_benchmark_OL1.txt -------------------------------------------------------------------------------- /benchmarking/benchmarking_files/HISAT/HISAT_perfect/GLM_output_benchmark_OL1.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/benchmarking/benchmarking_files/HISAT/HISAT_perfect/GLM_output_benchmark_OL1.txt -------------------------------------------------------------------------------- /benchmarking/count_tables.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/benchmarking/count_tables.py -------------------------------------------------------------------------------- /benchmarking/figure_1E.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/benchmarking/figure_1E.R -------------------------------------------------------------------------------- /benchmarking/shared_concordance.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/benchmarking/shared_concordance.py -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/requirements.txt -------------------------------------------------------------------------------- /scripts/GLM_script_light.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/scripts/GLM_script_light.R -------------------------------------------------------------------------------- /scripts/Process_CI_10x.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/scripts/Process_CI_10x.py -------------------------------------------------------------------------------- /scripts/__pycache__/annotator.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/scripts/__pycache__/annotator.cpython-36.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/annotator.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/scripts/__pycache__/annotator.cpython-37.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/light_utils.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/scripts/__pycache__/light_utils.cpython-36.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/light_utils.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/scripts/__pycache__/light_utils.cpython-37.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/utils_juncReads_minimal.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/scripts/__pycache__/utils_juncReads_minimal.cpython-36.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/utils_juncReads_minimal.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/scripts/__pycache__/utils_juncReads_minimal.cpython-37.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/utils_juncReads_minimal_HISAT.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/scripts/__pycache__/utils_juncReads_minimal_HISAT.cpython-36.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/utils_os.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/scripts/__pycache__/utils_os.cpython-36.pyc -------------------------------------------------------------------------------- /scripts/__pycache__/utils_os.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/scripts/__pycache__/utils_os.cpython-37.pyc -------------------------------------------------------------------------------- /scripts/ann_splices.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/scripts/ann_splices.py -------------------------------------------------------------------------------- /scripts/annotator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/scripts/annotator.py -------------------------------------------------------------------------------- /scripts/annotator.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/scripts/annotator.pyc -------------------------------------------------------------------------------- /scripts/consolidate_GLM_output_files.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/scripts/consolidate_GLM_output_files.R -------------------------------------------------------------------------------- /scripts/create_annotator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/scripts/create_annotator.py -------------------------------------------------------------------------------- /scripts/light_class_input.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/scripts/light_class_input.py -------------------------------------------------------------------------------- /scripts/light_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/scripts/light_utils.py -------------------------------------------------------------------------------- /scripts/post_processing.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/scripts/post_processing.R -------------------------------------------------------------------------------- /scripts/utils_os.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/scripts/utils_os.py -------------------------------------------------------------------------------- /scripts/view_seqs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/salzman-lab/SICILIAN/HEAD/scripts/view_seqs.py --------------------------------------------------------------------------------