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FreeRTOS.txt
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FreeRTOS.txt
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橙 Data 腔恅璃標 PATH 蹈桶
橙唗蹈瘍峈 A694-DF88
D:.
岫 FreeRTOS.txt
岫 generated directory.bat
岫 README.md
岫
念岸.idea
岫 岫 .gitignore
岫 岫 .name
岫 岫 misc.xml
岫 岫 modules.xml
岫 岫 SCARP.iml
岫 岫 workspace.xml
岫 岫
岫 弩岸inspectionProfiles
岫 profiles_settings.xml
岫 Project_Default.xml
岫
念岸docs
岫 pipeline.svg
岫
念岸Exp1_Benchmark
岫 岫 README.md
岫 岫 S01_Data_Preprocessing.ipynb
岫 岫 S02_Run_SCARP.ipynb
岫 岫
岫 念岸.ipynb_checkpoints
岫 岫 S01_Data_Preprocessing-checkpoint.ipynb
岫 岫 S02_Run_SCARP-checkpoint.ipynb
岫 岫
岫 念岸figures
岫 岫 tsne_blood2K_labeled.svg
岫 岫 tsne_Breast_Tumor_labeled.svg
岫 岫 tsne_Forebrain_labeled.svg
岫 岫 tsne_GM12878vsHEK_labeled.svg
岫 岫 tsne_GM12878vsHL_labeled.svg
岫 岫 tsne_InSilico_labeled.svg
岫 岫 tsne_Leukemia_labeled.svg
岫 岫 tsne_Sox10KD_labeled.svg
岫 岫 tsne_Splenocyte_labeled.svg
岫 岫 umap_blood2K_labeled.svg
岫 岫 umap_blood2K_louvain.svg
岫 岫 umap_Breast_Tumor_labeled.svg
岫 岫 umap_Breast_Tumor_louvain.svg
岫 岫 umap_Forebrain_labeled.svg
岫 岫 umap_Forebrain_louvain.svg
岫 岫 umap_GM12878vsHEK_labeled.svg
岫 岫 umap_GM12878vsHEK_louvain.svg
岫 岫 umap_GM12878vsHL_labeled.svg
岫 岫 umap_GM12878vsHL_louvain.svg
岫 岫 umap_InSilico_labeled.svg
岫 岫 umap_InSilico_louvain.svg
岫 岫 umap_Leukemia_labeled.svg
岫 岫 umap_Leukemia_louvain.svg
岫 岫 umap_Sox10KD_labeled.svg
岫 岫 umap_Sox10KD_louvain.svg
岫 岫 umap_Splenocyte_labeled.svg
岫 岫 umap_Splenocyte_louvain.svg
岫 岫
岫 念岸Processed data
岫 岫 blood2K.h5ad
岫 岫 Breast_Tumor.h5ad
岫 岫 Forebrain.h5ad
岫 岫 GM12878vsHEK.h5ad
岫 岫 GM12878vsHL.h5ad
岫 岫 InSilico.h5ad
岫 岫 Leukemia.h5ad
岫 岫 Sox10KD.h5ad
岫 岫 Splenocyte.h5ad
岫 岫
岫 念岸Raw data
岫 岫 岫 Breast_Tumor.h5ad
岫 岫 岫 Forebrain.h5ad
岫 岫 岫 GM12878vsHEK.h5ad
岫 岫 岫 GM12878vsHL.h5ad
岫 岫 岫 InSilico.h5ad
岫 岫 岫 Leukemia.h5ad
岫 岫 岫 Splenocyte.h5ad
岫 岫 岫
岫 岫 念岸blood2K
岫 岫 岫 Filter_Cells.txt
岫 岫 岫 Filter_df.txt
岫 岫 岫 Filter_Peaks.txt
岫 岫 岫 metadata.txt
岫 岫 岫
岫 岫 弩岸SOX10
岫 岫 GSE114557_MM057_MM087_Sox10KD_GoodCells_mergedPeaks_correctformat.counts.txt
岫 岫 GSE114557_MM057_MM087_Sox10KD_GoodCells_mergedPeaks_correctformat.counts.txt.gz
岫 岫
岫 弩岸Results
岫 Kept component of blood2K.svg
岫 Kept component of Forebrain.svg
岫 Kept component of GM12878vsHEK.svg
岫 Kept component of GM12878vsHL.svg
岫 Kept component of InSilico.svg
岫 Kept component of Leukemia.svg
岫 Kept component of Sox10KD.svg
岫 Kept component of Splenocyte.svg
岫 Louvain confusion mat of blood2K.svg
岫 Louvain confusion mat of Breast_Tumor.svg
岫 Louvain confusion mat of Forebrain.svg
岫 Louvain confusion mat of GM12878vsHEK.svg
岫 Louvain confusion mat of GM12878vsHL.svg
岫 Louvain confusion mat of InSilico.svg
岫 Louvain confusion mat of Leukemia.svg
岫 Louvain confusion mat of Sox10KD.svg
岫 Louvain confusion mat of Splenocyte.svg
岫
念岸Exp2_Robustness
岫 岫 S01_Filter_peaks.ipynb
岫 岫 S02_Run_SCARP.ipynb
岫 岫
岫 念岸.ipynb_checkpoints
岫 岫 S01_Filter_peaks-checkpoint.ipynb
岫 岫 S02_Run_SCARP-checkpoint.ipynb
岫 岫 S02_Run_SCARP_to _test_robustness-checkpoint.ipynb
岫 岫
岫 念岸Processed data
岫 岫 blood2K_filter30.h5ad
岫 岫 blood2K_filter40.h5ad
岫 岫 blood2K_filter50.h5ad
岫 岫 blood2K_filter60.h5ad
岫 岫 blood2K_filter70.h5ad
岫 岫 blood2k_filter_var0.5.h5ad
岫 岫 blood2k_filter_var0.6.h5ad
岫 岫 blood2k_filter_var0.7.h5ad
岫 岫 blood2k_filter_var0.8.h5ad
岫 岫 blood2k_filter_var0.9.h5ad
岫 岫 Sox10KD_filter10.h5ad
岫 岫 Sox10KD_filter20.h5ad
岫 岫 Sox10KD_filter30.h5ad
岫 岫 Sox10KD_filter40.h5ad
岫 岫 Sox10KD_filter50.h5ad
岫 岫 Sox10KD_filter_var0.5.h5ad
岫 岫 Sox10KD_filter_var0.6.h5ad
岫 岫 Sox10KD_filter_var0.7.h5ad
岫 岫 Sox10KD_filter_var0.8.h5ad
岫 岫 Sox10KD_filter_var0.9.h5ad
岫 岫
岫 弩岸Results
岫 blood2k_louvain_ARI_score.txt
岫 blood2k_louvain_NMI_score.txt
岫 blood2k_peaksnum.svg
岫 blood2k_Score.svg
岫 blood2k_time.svg
岫 Sox10KD_louvain_ARI_score.txt
岫 Sox10KD_louvain_NMI_score.txt
岫 Sox10KD_peaksnum.svg
岫 Sox10KD_Score.svg
岫 Sox10KD_time.svg
岫
念岸Exp3_SNARE_seq
岫 岫 README.md
岫 岫 S01_Signac_vignette.R
岫 岫 S02_Run_SCARP.ipynb
岫 岫 S03_Cells_clustering.R
岫 岫 SNARE.Rproj
岫 岫
岫 念岸Processed data
岫 念岸Raw data
岫 岫 念岸GSE126074_AdBrainCortex_atac
岫 岫 岫 barcodes.tsv.gz
岫 岫 岫 features.tsv.gz
岫 岫 岫 fragments.sort.bed.gz
岫 岫 岫 fragments.sort.bed.gz.tbi
岫 岫 岫 GSE126074_AdBrainCortex_SNAREseq_chromatin.barcodes.tsv.gz
岫 岫 岫 GSE126074_AdBrainCortex_SNAREseq_chromatin.counts.mtx.gz
岫 岫 岫 GSE126074_AdBrainCortex_SNAREseq_chromatin.peaks.tsv.gz
岫 岫 岫 matrix.mtx.gz
岫 岫 岫
岫 岫 弩岸GSE126074_AdBrainCortex_rna
岫 岫 allen_brain.rds
岫 岫 barcodes.tsv.gz
岫 岫 features.tsv.gz
岫 岫 GSE126074_AdBrainCortex_SNAREseq_cDNA.barcodes.tsv.gz
岫 岫 GSE126074_AdBrainCortex_SNAREseq_cDNA.counts.mtx.gz
岫 岫 GSE126074_AdBrainCortex_SNAREseq_cDNA.genes.tsv.gz
岫 岫 matrix.mtx.gz
岫 岫
岫 弩岸Results
岫 Cells_filtered.csv
岫 cisTopic_silhouette.svg
岫 cisTOPIC_uamp.svg
岫 Kept component of AdBrainCortex.svg
岫 RNA_silhouette.svg
岫 RNA_umap.svg
岫 scAND_silhouette.svg
岫 scAND_umap.svg
岫 SCARP_ATAC_Cells_df.txt
岫 SCARP_silhouette.svg
岫 SCARP_umap.svg
岫 SNARE_Celltype.csv
岫
念岸Exp4_SOX10_Knockdown
岫 岫 Exp4_SOX10_Knockdown.Rproj
岫 岫 README.md
岫 岫 S01_Run_SCARP.ipynb
岫 岫 S02_Peak annotation.R
岫 岫 S03_Computing_coaccessible_peaks.ipynb
岫 岫 S04_Gene_Enrichment.R
岫 岫 S05_Survival_analysis.R
岫 岫
岫 念岸.ipynb_checkpoints
岫 岫 S01_Data_Preprocessing-checkpoint.ipynb
岫 岫 S01_Run_SCARP-checkpoint.ipynb
岫 岫 S02_Computing_coaccessible_peaks-checkpoint.ipynb
岫 岫 S02_Run_SCARP-checkpoint.ipynb
岫 岫 S03_Computing_coaccessible_peaks-checkpoint.ipynb
岫 岫
岫 念岸figures
岫 岫 Distribution of ATAC-seq loci relative to TSS (only promoters).svg
岫 岫 Distribution of ATAC-seq loci relative to TSS.svg
岫 岫 dotplot_Co-accessible loci of SOX10 by cisTOPIC.svg
岫 岫 dotplot_Co-accessible loci of SOX10 by original.svg
岫 岫 dotplot_Co-accessible loci of SOX10 by scAND.svg
岫 岫 dotplot_Co-accessible loci of SOX10 by SCARP.svg
岫 岫 pieplot(promoter).svg
岫 岫 pieplot.svg
岫 岫 upsetplot(promoter).svg
岫 岫 upsetplot.svg
岫 岫
岫 念岸Processed data
岫 岫 annotated_genes_1000bp.csv
岫 岫 annotated_genes_1000bp_alltype.csv
岫 岫 Sox10KD_peaks.bed
岫 岫
岫 念岸Results
岫 岫 岫 cisTopic_diff_access_sites_top50.csv
岫 岫 岫 KEGG_cisTopic.svg
岫 岫 岫 KEGG_cnetplot_cisTopic.svg
岫 岫 岫 KEGG_cnetplot_original.svg
岫 岫 岫 KEGG_cnetplot_scAND.svg
岫 岫 岫 KEGG_cnetplot_SCARP.svg
岫 岫 岫 KEGG_original.svg
岫 岫 岫 KEGG_scAND.svg
岫 岫 岫 KEGG_SCARP.svg
岫 岫 岫 Kept component of Sox10KD.svg
岫 岫 岫 original_diff_access_sites_top50.csv
岫 岫 岫 SCAND_diff_access_sites_top50.csv
岫 岫 岫 SCARP_diff_access_sites_top50.csv
岫 岫 岫 SOX10_SCARP_Cells_feature.csv
岫 岫 岫 SOX10_SCARP_Peaks_feature.csv
岫 岫 岫
岫 岫 弩岸cytoscape
岫 岫 cisTOPIC default edge.csv
岫 岫 cisTOPIC default node.csv
岫 岫 cisTOPIC.cys
岫 岫 cisTOPIC.pdf
岫 岫 cisTopic_diff_access_sites_top50.csv
岫 岫 original default edge.csv
岫 岫 original default node.csv
岫 岫 original.cys
岫 岫 original.pdf
岫 岫 original_diff_access_sites_top50.csv
岫 岫 scand default edge.csv
岫 岫 scand default node.csv
岫 岫 scAND.cys
岫 岫 scAND.pdf
岫 岫 SCAND_diff_access_sites_top50.csv
岫 岫 SCARP default edge.csv
岫 岫 scarp default node.csv
岫 岫 SCARP.cys
岫 岫 SCARP.pdf
岫 岫 SCARP_diff_access_sites_top50.csv
岫 岫
岫 念岸Survival result
岫 岫 AKAP13.svg
岫 岫 COQ10B.svg
岫 岫 CTBP2.svg
岫 岫 FAM227B.svg
岫 岫 FBXO38.svg
岫 岫 MITF.svg
岫 岫 P4HTM.svg
岫 岫 SLC14A2.svg
岫 岫 STK17B.svg
岫 岫 SYT11.svg
岫 岫 TRIM69.svg
岫 岫 XPNPEP3.svg
岫 岫 ZC3H6.svg
岫 岫 ZCCHC24.svg
岫 岫
岫 弩岸TCGA
岫 survival_SKCM_survival.txt
岫 TCGA-SKCM.htseq_fpkm.tsv
岫 TCGA-SKCM.htseq_fpkm.tsv.gz
岫
念岸Exp5_10X_Multiome
岫 岫 help_func.py
岫 岫 README.md
岫 岫 S01_Data_Preprocessing.ipynb
岫 岫 S02_Run_SCARP_CD4naive.ipynb
岫 岫 S03_PCHIC_Enhancer_CD4naive.ipynb
岫 岫 S04_Chip_Seq.ipynb
岫 岫 S05_Differential_Analysis.ipynb
岫 岫
岫 念岸.ipynb_checkpoints
岫 岫 Data preprocessing-checkpoint.ipynb
岫 岫 Differential analysis-checkpoint.ipynb
岫 岫 Run SCARP-checkpoint.ipynb
岫 岫 S01_Data_Preprocessing-checkpoint.ipynb
岫 岫 S02_Run_SCARP-checkpoint.ipynb
岫 岫 S03_PCHIC-checkpoint.ipynb
岫 岫 S04_Chip_Seq-checkpoint.ipynb
岫 岫 S05_Differential_Analysis-checkpoint.ipynb
岫 岫
岫 念岸figures
岫 岫 stacked_violin__ATAC_CD14_Mono_marker_peaks.svg
岫 岫 stacked_violin__RNA_CD14Mono_marker_genes.svg
岫 岫 umap10X_pbmc_ATAC_celltype_filteredlabel.svg
岫 岫 umap_CD14_Mono_cells.svg
岫 岫 violin_ATAC_CD14_Mono_violin_group0.svg
岫 岫 violin_ATAC_CD14_Mono_violin_group1.svg
岫 岫 violin_RNA_CD14_Mono_violin_group0.svg
岫 岫 violin_RNA_CD14_Mono_violin_group1.svg
岫 岫
岫 念岸Processed data
岫 岫 10X_pbmc_ATAC.h5ad
岫 岫 10X_pbmc_ATAC_celltype_filtered.h5ad
岫 岫 10X_pbmc_ATAC_celltype_filtered_CD4_Naive.h5ad
岫 岫 10X_pbmc_ATAC_celltype_filtered_CD8_Naive.h5ad
岫 岫 10X_pbmc_RNA.h5ad
岫 岫
岫 念岸Raw data
岫 岫 岫 ActivePromoterEnhancerLinks.tsv
岫 岫 岫 pbmc_granulocyte_sorted_10k_atac_peak_annotation.tsv
岫 岫 岫 pbmc_granulocyte_sorted_10k_filtered_feature_bc_matrix.h5
岫 岫 岫 PCHiC_peak_matrix_cutoff5.tsv
岫 岫 岫 wnn_meta_data.csv
岫 岫 岫
岫 岫 弩岸Human_hg19
岫 岫 Digest_Human_HindIII.rmap
岫 岫 Digest_Human_HindIII_baits_e75_ID.baitmap
岫 岫 Human_HindIII_NBaitsPerBin.nbpb
岫 岫 Human_HindIII_NperBin.npb
岫 岫 Human_HindIII_proxOE.poe
岫 岫
岫 念岸Results
岫 岫 10X_pbmc_ATAC_celltype_filtered_SCARP_Cells_feature.csv
岫 岫 10X_pbmc_ATAC_celltype_filtered_SCARP_Cells_feature_CD4_Naive.csv
岫 岫 10X_pbmc_ATAC_celltype_filtered_SCARP_Cells_feature_CD8_Naive.csv
岫 岫 10X_pbmc_ATAC_celltype_filtered_SCARP_Peaks_feature.csv
岫 岫 10X_pbmc_ATAC_celltype_filtered_SCARP_Peaks_feature_CD4_Naive.csv
岫 岫 10X_pbmc_ATAC_celltype_filtered_SCARP_Peaks_feature_CD8_Naive.csv
岫 岫 10X_pbmc_ATAC_SCARP_Cells_feature.csv
岫 岫 10X_pbmc_ATAC_SCARP_Peaks_feature.csv
岫 岫 CD8 Naive.svg
岫 岫
岫 弩岸__pycache__
岫 help_func.cpython-38.pyc
岫
弩岸Scarp
岫 data_preprocessing.py
岫 downstream.py
岫 SCARP_help_func.py
岫
弩岸__pycache__
data_preprocessing.cpython-38.pyc
downstream.cpython-38.pyc
SCARP_help_func.cpython-38.pyc