├── 01_rMATS_on_BAM_file ├── 01_rMATS_on_BAM_file.sh └── README.txt ├── 02_PSI_value_quantification ├── .DS_Store ├── 01_Get_PSI_from_rMATS_output │ ├── Get_PSI_from_rMATS_output.R │ ├── example_input │ │ ├── JC.raw.input.A3SS.txt │ │ ├── JC.raw.input.A5SS.txt │ │ ├── JC.raw.input.MXE.txt │ │ ├── JC.raw.input.RI.txt │ │ ├── JC.raw.input.SE.txt │ │ ├── JCEC.raw.input.A3SS.txt │ │ ├── JCEC.raw.input.A5SS.txt │ │ ├── JCEC.raw.input.MXE.txt │ │ ├── JCEC.raw.input.RI.txt │ │ ├── JCEC.raw.input.SE.txt │ │ ├── fromGTF.A3SS.txt │ │ ├── fromGTF.A5SS.txt │ │ ├── fromGTF.MXE.txt │ │ ├── fromGTF.RI.txt │ │ ├── fromGTF.SE.txt │ │ ├── fromGTF.novelEvents.A3SS.txt │ │ ├── fromGTF.novelEvents.A5SS.txt │ │ ├── fromGTF.novelEvents.MXE.txt │ │ ├── fromGTF.novelEvents.RI.txt │ │ └── fromGTF.novelEvents.SE.txt │ └── example_output │ │ ├── SE_JC_IC_filter.txt │ │ ├── SE_JC_PSI_filter.txt │ │ └── SE_JC_totalRC_filter.txt ├── 02_Imputation │ ├── PSI_imputation.R │ └── example_output │ │ └── SE_JC_impute_PSI_filter_KNN.txt └── README.txt ├── 03_Get_sample_annotation ├── Get_sample_annotation.R ├── README.txt ├── example_input │ ├── GTEx_v7_Annotations_SampleAttributesDS.txt │ ├── GTEx_v7_Annotations_SubjectPhenotypesDS.txt │ └── gtex_v7_brain.csv └── example_output │ ├── agetable_brain.txt │ ├── batch_effect_table_brain.txt │ ├── brain_region_table_brain.txt │ ├── gendertable_brain.txt │ └── sampleID_SRRID_brain.txt ├── 04_tSNE_on_PSI ├── README.txt ├── example_input │ └── phs000424.v7.pht002742.v7.p2.c1.GTEx_Subject_Phenotypes.GRU.txt ├── example_output │ ├── SE_JC_tsne_sample_logit_PSI.txt │ └── logit_SE_JC_t-SNE_plot.pdf ├── t-SNE_on_PSI_calculation.R └── t-SNE_on_PSI_plot.R ├── 05_Differential_splicing_analysis ├── .DS_Store ├── 01_SVA │ ├── DS_analysis_SVA.R │ └── example_output │ │ ├── SE_JC_SVA_brain_gender_age_pprob.b.txt │ │ ├── SE_JC_SVA_brain_gender_age_pprob.gam.txt │ │ └── SE_JC_SVA_brain_gender_age_surrogate_variable.txt ├── 02_linear_mixed_model │ ├── example_output │ │ ├── betamatrix_lmm_output_no_interaction_no_warning_one_full_model_original_age_imputed_psi_no_weight_JC_oneforall_original_region_with_SVA.txt │ │ └── pvmatrix_lmm_output_no_interaction_no_warning_one_full_model_original_age_imputed_psi_no_weight_JC_oneforall_original_region_with_SVA.txt │ ├── lmm_output_no_interaction_no_warning_one_full_model_original_age_imputed_psi_no_weight_JC_oneforall_original_region_with_SVA.R │ └── lmm_output_no_interaction_no_warning_one_full_model_original_age_imputed_psi_no_weight_JC_oneforall_original_region_with_SVA.cmd ├── 03_summary_and_plot │ ├── DS_analysis_lmm_plot.R │ ├── DS_analysis_lmm_summary.R │ ├── README.txt │ └── example_output │ │ ├── A3SS_BR_dependent_splicing_event_summary.txt │ │ ├── A5SS_AGE_dependent_splicing_event_summary.txt │ │ ├── A5SS_BR_dependent_splicing_event_summary.txt │ │ ├── Number_of_significant_event_all_splicetype_all_phenotype.pdf │ │ ├── SE_AGE_dependent_splicing_event_summary.txt │ │ └── SE_BR_dependent_splicing_event_summary.txt └── README.txt ├── 06_Genotype_PCA ├── 1_generate_binary_genotype_file.sh ├── 2_PCA_on_genotype_EIGENSTRAT.sh ├── 3_PCA_result_visualization.R └── README.txt ├── 07_SVA_on_PSI_for_sQTL_analysis ├── .Rhistory ├── README.txt └── SVA_on_PSI_for_sQTL_analysis.R ├── 08_Correction_for_technical_confounders ├── Correction_for_technical_confounders.R └── README.txt ├── 09_sQTL_analysis ├── .DS_Store ├── 01_Genome_wide_LD_calculation_1000Genome │ ├── 01_vcf2plink.sh │ ├── 02_Genome_wide_LD_calculation.sh │ └── submit_LD.sh ├── 02_Genotype_data_processing │ └── Genotype_data_processing.sh ├── 03_sQTL_calculation │ ├── 0_glmm_input.R │ ├── 1_my_generateRaw_V7.py │ ├── 2_split_raw_file_each_chr.py │ ├── 3_make.submission.py │ ├── 4_qsub.glimmps.sh │ ├── 5_selectSNPsByEvents_permutation.R │ ├── 5_selectSNPsByEvents_pvalue.py │ ├── 6_convertGPos2rsID.py │ ├── 7_run_plink_old.sh │ ├── 8_gwas_linkage_NHGRI.py │ ├── GLiMMPS_functions.R │ ├── README.md │ ├── brainregionlist.txt │ ├── chroms.txt │ ├── pipeline_part1.sh │ ├── pipeline_part2.sh │ ├── pipeline_part3.sh │ ├── sQTLregress.oneexon.cis.R │ ├── sQTLregress.oneexon.cis.perm.R │ ├── submit_0_glmm_input.sh │ └── submit_pipeline.sh ├── 04_sQTL_summary │ ├── 9_sQTL_result_summary_more_stringent.R │ └── sQTL_result_summary.R ├── 05_sQTL_result_plot │ ├── 1_sQTL_result_significant_event_plot.R │ ├── 2_sQTL_result_all_event_summary.R │ ├── 3_sQTL_result_sashimi_plot_index.sh │ ├── 4_sQTL_result_sashimi_plot.R │ ├── 5_sQTL_result_LocusZoom_plot.R │ └── 5_sQTL_result_LocusZoom_plot_rsID_conversion.py └── README.txt ├── 10_Positional_distribution_of_sQTLs ├── .DS_Store ├── 01_SNP_distribution │ └── SNP_distribution.R ├── 02_Fraction_of_exon_within_300bp │ ├── 1_Fraction_of_exon_within_300bp.R │ ├── 2_Fraction_of_exon_within_300bp_plot.R │ └── brainregionlist.txt ├── 03_SNP_position_distribution_vs_SNP_significance │ └── SNP_position_distribution_vs_SNP_significance.R ├── 04_SNP_significance_vs_brain_region_specificity │ └── sQTL_significance_vs_brain_region_specificity.R ├── 05_SNP_position_distribution_vs_brain_region_specificity │ ├── .Rhistory │ ├── 1_SNP_to_SS_distance_vs_brain_region_specificity - 5 categories.R │ ├── 2_SNP_to_SS_distance_vs_brain_region_specificity - 5 categories - cdf plot - more stringent cutoff.R │ └── 2_SNP_to_SS_distance_vs_brain_region_specificity - 5 categories - circular barplot - more stringent cutoff.R └── README.txt ├── 11_Gene_expression_preprocessing ├── Gene_expression_data_preprocessing.R └── README.txt ├── 12_tSNE_on_gene_expression ├── README.txt ├── t-SNE_on_gene_expression_calculation.R └── t-SNE_on_gene_expression_plot.R ├── 13_Differential_expression_analysis ├── .DS_Store ├── 01_SVA │ └── Gene_expression_SVA.R ├── 02_linear_mixed_model │ └── lmm_output_no_interaction_no_warning_one_full_model_original_age_oneforall_original_region_without_SVA.R ├── 03_summary_and_plot │ ├── DE_analysis_lmm_plot.R │ └── DE_analysis_lmm_summary.R └── README.txt ├── 14_RBP_binding_analysis ├── .DS_Store ├── 01_Heatmap_of_RBP_expression │ └── Heatmap_of_RBP_expression.R ├── 02_Generate_job_list │ └── Generate_job_list.R ├── 03_Heatmap_of_beta_value_of_all_sQTLs_and_plot_for_individual_examples │ └── Heatmap_of_beta_value_of_all_sQTLs_and_plot_for_individual_examples.R ├── 04_DeepBind_on_all_SNP_all_RBP │ ├── DeepBind_on_all_SNP_all_RBP.R │ └── rbp_map_functions.py ├── 05_DeepBind_result_summary_and_plot │ ├── 1_DeepBind_mutation_map.R │ ├── 2_DeepBind_on_all_SNP_all_RBP_result_summary.R │ └── 3_DeepBind_summary_plot_per_exon.R ├── 06_Differential_RBP_expression │ ├── 1_DeepBind_region_dependent_sQTL_RBP_calculation.R │ └── 2_DeepBind_region_dependent_sQTL_RBP_plot.R ├── 07_Individual_RBP_motif_scan_and_plot │ ├── Individual_RBP_motif_scan.R │ └── Individual_RBP_motif_scan_plot.R ├── README.txt └── heatmap.3.R ├── 15_region_ubiquitous_vs_specific_splicing_event_heatmap_radar_plot ├── .Rhistory ├── 1_Region_ubiquitous_vs_specific_splicing_event_heatmap_radar_plot_step_1_check_genotype_swap.R ├── 2_Region_ubiquitous_vs_specific_splicing_event_heatmap_radar_plot_step_2_collect_values_for_heatmap.R ├── 3_Region_ubiquitous_vs_specific_splicing_event_heatmap_radar_plot_step_3_pick_SNP_and_collect_values_for_heatmap_more_stringent_version_combine_result_single_job.R ├── 4_Region_ubiquitous_vs_specific_splicing_event_heatmap_radar_plot_step_3_pick_SNP_and_collect_values_for_heatmap_more_stringent_version_single_job.R ├── 5_Region_ubiquitous_vs_specific_splicing_event_heatmap_radar_plot_step_4_classification_and_plot_more_stringent_version.R └── README.txt ├── 16_Colocalization ├── .DS_Store ├── 0_search_and_download_summary_statistics │ ├── 0_Total_num_GWAS_studies.R │ ├── 1_Search_summary_statistics.R │ ├── 2_Download_summary_statistics.R │ └── 3_Summary_of_downloadable_GWAS_studies.R ├── 1_MAF_calculation │ └── 1_MAC_calculation.R ├── 2_Colocalization_input │ └── 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