├── .gitignore ├── LICENSE ├── README.md ├── code ├── DE-Workflow-Implementation │ ├── BEC_scanorama.py │ ├── BEC_scgen.py │ ├── BEC_scvi.py │ ├── _data_plot.R │ ├── _sample_run.R │ └── ref_script │ │ ├── BEC_QP.R │ │ ├── BEC_RISC.R │ │ ├── BEC_Seurat.R │ │ ├── BEC_combat.R │ │ ├── BEC_format_python_output.R │ │ ├── BEC_limma_bec.R │ │ ├── BEC_limmatrend_BECdata.R │ │ ├── BEC_mnn.R │ │ ├── BEC_pseudobulk.R │ │ ├── BEC_scmerge.R │ │ ├── BEC_zinbwave.R │ │ ├── COV_DESeq2.R │ │ ├── COV_DESeq2_zinbwavedata.R │ │ ├── COV_MAST.R │ │ ├── COV_edgeR.R │ │ ├── COV_edgeR_zinbwavedata.R │ │ ├── COV_limmatrend.R │ │ ├── COV_limmavoom.R │ │ ├── DE_Wilcoxson.R │ │ ├── META_DESeq2_sepdata.R │ │ ├── META_ES.R │ │ ├── META_FEM.R │ │ ├── META_LogNormalize.R │ │ ├── META_REM.R │ │ ├── META_edgeR_sepdata.R │ │ ├── META_limmatrend_sepdata.R │ │ └── META_wFisher.R ├── Data-Preparation │ ├── COVID19-data │ │ └── Preprocess_scRNAseq_COVID19.R │ ├── LUAD-data │ │ ├── BulkSampleAnalysis(Microarray).R │ │ ├── BulkSampleAnalysis(TCGA_LUAD).R │ │ └── Preprocess_scRNAseq_LUAD.R │ ├── model-based-simulation │ │ ├── model-based-simulation-2-batches-lowdepth.R │ │ ├── model-based-simulation-2-batches.R │ │ └── model-based-simulation-7-batches.R │ └── model-free-simulation │ │ ├── Model-free-simulation-with-Pancreas-data-beta-cells.md │ │ └── Model-free-simulation-with-Pancreas-data-beta-cells_files │ │ └── figure-gfm │ │ ├── unnamed-chunk-15-1.png │ │ ├── unnamed-chunk-3-1.png │ │ ├── unnamed-chunk-5-1.png │ │ ├── unnamed-chunk-7-1.png │ │ └── unnamed-chunk-8-1.png └── Result-Evaluation │ ├── COVID19-LUAD-Analysis │ ├── C0152013_disease_gda_summary.tsv │ ├── CTD_D000077192_genes_20210713220641.tsv │ ├── EVAL_Draw_pauc_tks_barplot.R │ ├── EVAL_Functions for visualization.R │ ├── EVAL_Known disease gene selection.R │ ├── EVAL_Prognostic gene selection(survival_analysis).R │ ├── EVAL_Standard positive gene detection(plot curves).R │ ├── EVAL_Standard positive gene detection(truncated kolmogorov-smirnov).R │ ├── EVAL_Standard positive gene selection_GO-0051607.R │ ├── EVAL_corr_heatmap(compare two cluster).R │ ├── EVAL_corr_heatmap(scluad_TCGA).R │ ├── EVAL_preranked_GSEA(scluad_TCGA).R │ ├── EVAL_save_DEresult.R │ ├── EVAL_save_DEresult_for_summary.R │ ├── GO_Biological_Process_2021.txt │ ├── LUAD-GSE31210.microarray.limma.cov.txt │ ├── LUAD-GSE43458.microarray.limma.cov.txt │ ├── LUAD_standard_positive_pathways(wikipathway).csv │ ├── TCGA-LUAD.rnaseq.processed.htseq_count.DESeq2_Cov.txt │ ├── TCGA-LUAD.rnaseq.processed.htseq_count.edgeR_Cov.txt │ ├── TCGA-LUAD.rnaseq.processed.htseq_count.limmatrend_Cov.txt │ ├── TCGA-LUAD.rnaseq.processed.htseq_count.limmavoom_Cov.txt │ ├── WikiPathway_2021_Human.txt │ ├── _sample_run_all_methods.R │ ├── scCOVID19_Monocytes_DE_result.rda │ ├── scLUAD_Epithelial cells_DE_result.rda │ ├── survival_analysis_result.txt │ └── truncated kolmogorov-smirnov.R │ ├── Execution-Example-Two-Batch │ ├── EVAL_aupr_2b.R │ ├── EVAL_check_deg_sign_2b.R │ ├── EVAL_deg_qval_vs_logfc_analysis.R │ ├── EVAL_fbeta_2b.R │ ├── EVAL_fbeta_qval_logfc_2b.R │ ├── EVAL_summary_heatmap.R │ ├── data │ │ ├── simul1_dropout_37_b1_300_b2_750 │ │ │ ├── cellinfo.txt │ │ │ ├── counts.txt │ │ │ ├── cpu_time.txt │ │ │ ├── de__genes.txt │ │ │ ├── geneinfo.txt │ │ │ ├── true_down_genes.txt │ │ │ └── true_up_genes.txt │ │ ├── simul2_dropout_39_b1_300_b2_750 │ │ │ ├── cellinfo.txt │ │ │ ├── counts.txt │ │ │ ├── cpu_time.txt │ │ │ ├── de__genes.txt │ │ │ ├── geneinfo.txt │ │ │ ├── true_down_genes.txt │ │ │ └── true_up_genes.txt │ │ ├── simul3_dropout_37_b1_300_b2_750 │ │ │ ├── cellinfo.txt │ │ │ ├── counts.txt │ │ │ ├── cpu_time.txt │ │ │ ├── de__genes.txt │ │ │ ├── geneinfo.txt │ │ │ ├── true_down_genes.txt │ │ │ └── true_up_genes.txt │ │ ├── simul4_dropout_39_b1_300_b2_750 │ │ │ ├── cellinfo.txt │ │ │ ├── counts.txt │ │ │ ├── cpu_time.txt │ │ │ ├── de__genes.txt │ │ │ ├── geneinfo.txt │ │ │ ├── true_down_genes.txt │ │ │ └── true_up_genes.txt │ │ ├── simul5_dropout_37_b1_300_b2_750 │ │ │ ├── cellinfo.txt │ │ │ ├── counts.txt │ │ │ ├── cpu_time.txt │ │ │ ├── de__genes.txt │ │ │ ├── geneinfo.txt │ │ │ ├── true_down_genes.txt │ │ │ └── true_up_genes.txt │ │ ├── simul6_dropout_39_b1_300_b2_750 │ │ │ ├── cellinfo.txt │ │ │ ├── counts.txt │ │ │ ├── cpu_time.txt │ │ │ ├── de__genes.txt │ │ │ ├── geneinfo.txt │ │ │ ├── true_down_genes.txt │ │ │ └── true_up_genes.txt │ │ ├── sp80.simul1_dropout_37_b1_300_b2_750_full.RData │ │ ├── sp80.simul2_dropout_39_b1_300_b2_750_full.RData │ │ ├── sp80.simul3_dropout_37_b1_300_b2_750_full.RData │ │ ├── sp80.simul4_dropout_39_b1_300_b2_750_full.RData │ │ ├── sp80.simul5_dropout_37_b1_300_b2_750_full.RData │ │ └── sp80.simul6_dropout_39_b1_300_b2_750_full.RData │ └── heatmapdata.RDS │ └── Simulation-Analysis │ ├── EVAL_aupr_2b.R │ ├── EVAL_check_deg_sign_2b.R │ ├── EVAL_check_logfc_without_de_method.R │ ├── EVAL_deg_qval_vs_logfc_analysis.R │ ├── EVAL_fbeta_2b.R │ ├── 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