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risearch2
risearch2
 
 
.gitattributes
.gitattributes
 
 
.gitignore
.gitignore
 
 
1_make_seeds.py
1_make_seeds.py
 
 
2_run_targetscan_60.sh
2_run_targetscan_60.sh
 
 
3_custom_run_predicttargets.arguments
3_custom_run_predicttargets.arguments
 
 
3_custom_run_predicttargets.sh
3_custom_run_predicttargets.sh
 
 
3_custom_run_predicttargets.test_sh
3_custom_run_predicttargets.test_sh
 
 
3way_check_functions.R
3way_check_functions.R
 
 
4_run_makeX.sh
4_run_makeX.sh
 
 
5_mtx2rds.R
5_mtx2rds.R
 
 
auroc.R
auroc.R
 
 
bench_pint_whinter.sh
bench_pint_whinter.sh
 
 
binary_table_T_anonymised.csv.xz
binary_table_T_anonymised.csv.xz
 
 
collect_bench_stats.R
collect_bench_stats.R
 
 
convert_format.py
convert_format.py
 
 
data_generator.R
data_generator.R
 
 
explain_lethal_situation.R
explain_lethal_situation.R
 
 
generate_3way.R
generate_3way.R
 
 
generation_functions.R
generation_functions.R
 
 
hierarchy_effect.R
hierarchy_effect.R
 
 
inference_test.R
inference_test.R
 
 
makeX.py
makeX.py
 
 
make_all.sh
make_all.sh
 
 
make_data_files.R
make_data_files.R
 
 
new_generator.R
new_generator.R
 
 
pint_only_time.R
pint_only_time.R
 
 
plot.R
plot.R
 
 
plot_comparison_roc.R
plot_comparison_roc.R
 
 
plot_times.R
plot_times.R
 
 
predicttargets.py
predicttargets.py
 
 
process_all_3way.R
process_all_3way.R
 
 
process_antibio_ifx.R
process_antibio_ifx.R
 
 
process_bacteria_data.R
process_bacteria_data.R
 
 
process_infX.R
process_infX.R
 
 
process_rds_whinter.R
process_rds_whinter.R
 
 
readme.md
readme.md
 
 
regenerate_data.R
regenerate_data.R
 
 
sample_mat.rds
sample_mat.rds
 
 
simple_Y.R
simple_Y.R
 
 
summary_functions.R
summary_functions.R
 
 
varying_cores_test.sh
varying_cores_test.sh
 
 

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Benchmarking and data processing scripts.

Reproducing simulations

A compiled version of WHInter should be placed in ./WHInter.

Rscript regenerate_data.R
bash bench_pint_whinter.sh
Rscript collect_bench_stats.R
Rscript plot.R

InfectX

Requires the package normInfectX.

Rscript process_ifx.R

Antibiotic data

Assumes a table of SNVs and MIC is present in "binary_table_T_anonymised.csv".

unxz binary_table_T_anonymised.csv.xz
./process_bacteria_data.R
./process_antibio_ifx.R

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