Files in SciOmicsLab/PhenoComb
Phenotype Combinatorial Analysis
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
PhenoComb.Rproj
R/RcppExports.R
R/combinatorial_phenotypes_generation.R
R/combinatorial_phenotypes_generation_server.R
R/independent_phenotype_identification.R
R/independent_phenotype_identification_server.R
R/logging.R
R/statistical_comparisons.R
R/statistical_comparisons_server.R
R/utils.R
R/zzz.R
README.md
benchmarks/performance-benchmarks/.gitignore
benchmarks/performance-benchmarks/R_mem_measure.sh
benchmarks/performance-benchmarks/benchmark_analysis.R
benchmarks/performance-benchmarks/experiments.csv
benchmarks/performance-benchmarks/flowType_experiment_results.csv
benchmarks/performance-benchmarks/flowType_loop.sh
benchmarks/performance-benchmarks/flowType_outputs/flowType_bm_10.log
benchmarks/performance-benchmarks/flowType_outputs/flowType_bm_11.log
benchmarks/performance-benchmarks/flowType_outputs/flowType_bm_4.log
benchmarks/performance-benchmarks/flowType_outputs/flowType_bm_5.log
benchmarks/performance-benchmarks/flowType_outputs/flowType_bm_6.log
benchmarks/performance-benchmarks/flowType_outputs/flowType_bm_7.log
benchmarks/performance-benchmarks/flowType_outputs/flowType_bm_8.log
benchmarks/performance-benchmarks/flowType_outputs/flowType_bm_9.log
benchmarks/performance-benchmarks/run_combinatorics_benchmark.R
benchmarks/performance-benchmarks/run_flowType_benchmark.R
benchmarks/performance-benchmarks/synthetic_dataset_generation.R
docs/FlowJo_tutorial/FlowJo_Tutorial.md
docs/FlowJo_tutorial/img/fig1.png
docs/FlowJo_tutorial/img/fig2.png
docs/FlowJo_tutorial/img/fig3.png
docs/FlowJo_tutorial/img/fig4.png
examples/full_local_analysis.R
examples/full_server_analysis.R
man/PhenoComb.Rd
man/combinatorial_phenotype_counts.Rd
man/combinatorial_phenotype_counts_server.Rd
man/compute_statistically_relevant_phenotypes.Rd
man/count_markers.Rd
man/csv_read_n_sorted_phenotypes.Rd
man/find_phenotype.Rd
man/find_phenotype_in_file.Rd
man/get_independent_relevant_phenotypes.Rd
man/get_independent_relevant_phenotypes_server.Rd
man/make_phenotype_name.Rd
man/phenotype_to_numbers.Rd
man/process_cell_data.Rd
man/statistically_relevant_phenotypes_server.Rd
src/RcppExports.cpp
src/count_phenotypes.cpp
src/utils.cpp
tests/testdata/combinatorial_phenotypes/channel_data.csv
tests/testdata/combinatorial_phenotypes/combinatorics_test_data.csv
tests/testdata/combinatorial_phenotypes/sample_data.csv
tests/testdata/statistical_comparison/fake_counts_log.log
tests/testdata/statistical_comparison/fake_phenotype_counts.csv
tests/testthat.R
tests/testthat/test-combinatorial-phenotypes-server.R
tests/testthat/test-combinatorial-phenotypes.R
tests/testthat/test-process-data.R
tests/testthat/test-statistical-comparison-server.R
tests/testthat/test-statistical-comparison.R
tests/testthat/test-utils-c.R
validation/COVIDome/PhenoCombAnalysis/input/Sample_Info.csv
validation/COVIDome/PhenoCombAnalysis/input/Thresholds.csv
validation/COVIDome/PhenoCombAnalysis/input/Thresholds_CD45+CD14+.csv
validation/COVIDome/PhenoCombAnalysis/input/Thresholds_CD45+CD19+.csv
validation/COVIDome/PhenoCombAnalysis/input/Thresholds_CD45+CD3+.csv
validation/COVIDome/PhenoCombAnalysis/input/Thresholds_CD45+CD3-CD19-CD56-CD14-.csv
validation/COVIDome/PhenoCombAnalysis/input/Thresholds_CD45+CD56+.csv
validation/COVIDome/PhenoCombAnalysis/output_lineages/combinatorial_phenotypes_parent_CD45+CD3+.log
validation/COVIDome/PhenoCombAnalysis/output_lineages/independent_phenotypes_parent_CD45+CD14+.csv
validation/COVIDome/PhenoCombAnalysis/output_lineages/independent_phenotypes_parent_CD45+CD14+.log
validation/COVIDome/PhenoCombAnalysis/output_lineages/independent_phenotypes_parent_CD45+CD19+.csv
validation/COVIDome/PhenoCombAnalysis/output_lineages/independent_phenotypes_parent_CD45+CD19+.log
validation/COVIDome/PhenoCombAnalysis/output_lineages/independent_phenotypes_parent_CD45+CD3-CD19-CD56-CD14-.csv
validation/COVIDome/PhenoCombAnalysis/output_lineages/independent_phenotypes_parent_CD45+CD3-CD19-CD56-CD14-.log
validation/COVIDome/PhenoCombAnalysis/output_lineages/independent_phenotypes_parent_CD45+CD56+.csv
validation/COVIDome/PhenoCombAnalysis/output_lineages/independent_phenotypes_parent_CD45+CD56+.log
validation/COVIDome/results/compiled_lineage_results.csv
validation/COVIDome/scripts/covid_server_phenocomb_run_lineages.R
validation/COVIDome/scripts/lineage_results_plot.R
validation/HIV/PhenoCombAnalysis/input/sample_data.csv
validation/HIV/PhenoCombAnalysis/input/threshold_data.csv
validation/HIV/PhenoCombAnalysis/output/combinatorial_phenotypes.log
validation/HIV/PhenoCombAnalysis/output/independent_phenotypes_pval_0.0000005.csv
validation/HIV/PhenoCombAnalysis/output/independent_phenotypes_pval_0.0000005.log
validation/HIV/PhenoCombAnalysis/output/independent_phenotypes_pval_0.0000005_5000_phenotypes.csv
validation/HIV/PhenoCombAnalysis/output/independent_phenotypes_pval_0.0000005_5000_phenotypes.log
validation/HIV/PhenoCombAnalysis/output/paper_final_phenotypes_data_CD3+_parent.csv
validation/HIV/PhenoCombAnalysis/output/paper_original_phenotypes_dataCD3+_parent.csv
validation/HIV/PhenoCombAnalysis/output/significant_phenotypes.log
validation/HIV/PhenoCombAnalysis/output/significant_phenotypes_CD3+_parent.log
validation/HIV/scripts/bootstrap_run.R
validation/HIV/scripts/filter_samples.R
validation/HIV/scripts/full_server_analysis.R
validation/HIV/scripts/get_paper_phenotypes.R
validation/HIV/scripts/input_generation.R
