GitHub - sanjusinha7/Scripts_MolCharAAvsEA: Scripts used in "Higher prevalence of homologous recombination deficiency in tumors from African Americans"

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Scripts used in "Higher prevalence of homologous recombination deficiency in tumors from African Americans"

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Name		Name	Last commit message	Last commit date
Latest commit History 5 Commits
.DS_Store		.DS_Store
.Rename_this.R.swp		.Rename_this.R.swp
.gitattributes		.gitattributes
AbberantGenes_list_from_an_Assay_Both_Phases.R		AbberantGenes_list_from_an_Assay_Both_Phases.R
BPC_Test.R		BPC_Test.R
BPC_Test_Illumina.R		BPC_Test_Illumina.R
CHTP_Pred_for_Illumina.R		CHTP_Pred_for_Illumina.R
CNVExp_Corr_Plot.R		CNVExp_Corr_Plot.R
CNV_Method_Consistency_Score.R		CNV_Method_Consistency_Score.R
CNV_burden.R		CNV_burden.R
Chromotripsis_Pred.R		Chromotripsis_Pred.R
Chromotripsis_Pred_Apx.R		Chromotripsis_Pred_Apx.R
Chromotripsis_Pred_Apx_Phase2.R		Chromotripsis_Pred_Apx_Phase2.R
Chromotripsis_Pred_Phase2.R		Chromotripsis_Pred_Phase2.R
Comparison_of_freq_files.R		Comparison_of_freq_files.R
Cytoband_on_Survial.R		Cytoband_on_Survial.R
Cytoband_on_Survial_TCGA.R		Cytoband_on_Survial_TCGA.R
Drivers_Freq_inTCGA.R		Drivers_Freq_inTCGA.R
Events_Enrichment_Test.R		Events_Enrichment_Test.R
Expression_HRDmarker.R		Expression_HRDmarker.R
Figure1B.R		Figure1B.R
Figure1_Panel2.R		Figure1_Panel2.R
Figure3-Nov27.R		Figure3-Nov27.R
Figure6_Aug31.R		Figure6_Aug31.R
Final_Figure1.R		Final_Figure1.R
Finding_novel_Drivers.R		Finding_novel_Drivers.R
GIStiC_preperation.R		GIStiC_preperation.R
GI_validation_from_TCGA.R		GI_validation_from_TCGA.R
GIvsRace_correctingconfounding.R		GIvsRace_correctingconfounding.R
Germline_HRD_test_acrossRaces_Gtex.R		Germline_HRD_test_acrossRaces_Gtex.R
HRD_via_multiple_Methods.r		HRD_via_multiple_Methods.r
LOH_NCIMD.R		LOH_NCIMD.R
LOH_calculation_NCIMD.R		LOH_calculation_NCIMD.R
Mut_matrix.R		Mut_matrix.R
Novel_Drivers_Freq_inTCGA.R		Novel_Drivers_Freq_inTCGA.R
OncoPrint.R		OncoPrint.R
Oscillatory_Events_Enrichement_Test.R		Oscillatory_Events_Enrichement_Test.R
PD1_across_race.R		PD1_across_race.R
Plot_Figure5_DriversLandscape.R		Plot_Figure5_DriversLandscape.R
Plot_GlobalCNVMap.R		Plot_GlobalCNVMap.R
Plotting_CHTP_pattern.R		Plotting_CHTP_pattern.R
Preparing_gistic_forlungTCGA.R		Preparing_gistic_forlungTCGA.R
Racewise_Gene_Frequency_foragene_NCIMD.R		Racewise_Gene_Frequency_foragene_NCIMD.R
Repeat_analysis_with_inferred_ancestry.R		Repeat_analysis_with_inferred_ancestry.R
Supp_Figures.R		Supp_Figures.R
Survival_Analysis.R		Survival_Analysis.R
Testing_sig3_acrossRace.R		Testing_sig3_acrossRace.R
UCEC_test.R		UCEC_test.R
Updated_Figure1Aug29.R		Updated_Figure1Aug29.R
Validation_HSMap_Step2.R		Validation_HSMap_Step2.R
Viewing_Chtp_Events_details.R		Viewing_Chtp_Events_details.R
analyzing_CNV_burden.R		analyzing_CNV_burden.R
ancestry_based_TCGA_confirmation.R		ancestry_based_TCGA_confirmation.R
anonmyzation.R		anonmyzation.R
arm_level_events-plot.R		arm_level_events-plot.R
chtp_validation_from_TCGA (copy).R		chtp_validation_from_TCGA (copy).R
cor_wd_cnvProfile.R		cor_wd_cnvProfile.R
corr_CNV_Exp (copy).R		corr_CNV_Exp (copy).R
corr_CNV_Exp_Both_Phases.R		corr_CNV_Exp_Both_Phases.R
define_Exp_matched_Scale.R		define_Exp_matched_Scale.R
driver_lung_CNV_freq_across_races.R		driver_lung_CNV_freq_across_races.R
enrichment_wd_previous_reports.R		enrichment_wd_previous_reports.R
finding_chtp.R		finding_chtp.R
finding_cytobands.R		finding_cytobands.R
genotyping_fromoncoscan.R		genotyping_fromoncoscan.R
germline_HRD.R		germline_HRD.R
germline_HRD_genewise.R		germline_HRD_genewise.R
gistic_forlungTCGA.R		gistic_forlungTCGA.R
hClustering_of_arm_level_event.R		hClustering_of_arm_level_event.R
heatmap_Figure2.R		heatmap_Figure2.R
incosmic.R		incosmic.R
infer_ancestry.R		infer_ancestry.R
infer_tcga_ancestry_Oct5.R		infer_tcga_ancestry_Oct5.R
make_data_public.R		make_data_public.R
plot_all_germline_pathways_together.Rmd		plot_all_germline_pathways_together.Rmd
plot_all_germline_pathways_together.nb.html		plot_all_germline_pathways_together.nb.html
put_all_probes_together.R		put_all_probes_together.R
race_specific_corr_wd_exp.R		race_specific_corr_wd_exp.R
running_GISTIC.R		running_GISTIC.R
survfit_of_risk.R		survfit_of_risk.R
tcga_ancestry.R		tcga_ancestry.R
venn_diagrams_of_overlap.R		venn_diagrams_of_overlap.R
vwriting_freq_file.R		vwriting_freq_file.R
write_LUSCmatrix_forBrid.R		write_LUSCmatrix_forBrid.R
write_supptable_tcga_populationDistribution.R		write_supptable_tcga_populationDistribution.R