Preview

scTAM-seq-scripts
- CpG_selection
  - HhaI 1753 CpGs.txt
    
    2.0 MB
  - Markdown_to_plot_simulations.Rmd
    
    10.8 kB
- LICENSE
  
  1.1 kB
- README.md
  
  1.6 kB
- dropout_correction
  - basic.stan
    
    254 Bytes
  - run_dropout_correction.R
    
    3.4 kB
  - run_dropout_correction_BM.R
    
    4.2 kB
- manuscript
  - Figure1
    - F1_B_cut_vs_uncut.R
      
      5.4 kB
    - F1_C_basic_statistics.R
      
      3.6 kB
    - F1_D_heatmap.R
      
      3.0 kB
    - F1_E_bulk_comparison.R
      
      4.1 kB
    - F1_F_G_protein_analysis.R
      
      15.5 kB
  - Figure2
    - F2_A_heatmap.R
      
      7.0 kB
    - F2_C_UMAP.R
      
      5.4 kB
    - F2_D_protein_analysis.R
      
      6.8 kB
    - F2_E_chromatin_states.R
      
      8.2 kB
  - Figure3
    - F3_A_heatmap.R
      
      6.5 kB
    - F3_BC_UMAP.R
      
      6.9 kB
    - F3_D_f_integration.R
      
      22.7 kB
    - F3_G_protein_Seurat.R
      
      5.0 kB
  - Supplement
    - Supp_F15_imprinted.R
      
      4.2 kB
    - Supp_F2_basic_statistics.R
      
      3.5 kB
    - Supp_F2_cut_vs_uncut.R
      
      5.2 kB
    - Supp_F4_all_non_Hha_boxplots.R
      
      4.0 kB
    - Supp_F5_GC_content.R
      
      4.5 kB
    - Supp_F8_bulk_comparison.R
      
      4.0 kB
    - Supp_F9_BM_blood_comparison.R
      
      2.7 kB
    - Supp_Fig_1.R
      
      8.2 kB
    - Supp_Fig_8_pseudo_bulk.R
      
      3.9 kB
- misc
  - Blood.Bone.Marrow.Amplicons.design.dropout.added.selected.tsv
    
    128.8 kB
  - Code_array_samples_updated_220318.txt
    
    2.9 kB
  - Colors_ChromHMM.txt
    
    693 Bytes
  - CpGs.value.per.amplicon.Blood.Bone.marrow.complete.array.data.txt
    
    140.4 kB
  - GSM5935918_Blood_HhaI
    - tsv
      - rowinfo.csv
        
        5.7 MB
  - GSM5935920_Blood_undigested
    - tsv
      - doublet_scores_DoubletDetection.csv
        
        270.9 kB
  - GSM5935921_BM_HhaI
    - tsv
      - colinfo_BM.csv
        
        57.7 kB
      - rowinfo.csv
        
        3.2 MB
  - GSM5935923_BM_undigested
    - tsv
      - colinfo.csv
        
        21.7 kB
      - doublet_scores_DoubletDetection.csv
        
        335.9 kB
      - selected_amplicons.tsv
        
        60.1 kB
  - MBC_assignment.txt
    
    668 Bytes
  - amplicons_CpG_GC_annotated.csv
    
    137.7 kB
  - colinfo_diff_cells.chrom.states.RData
    
    9.3 kB
  - compute_imprinted_bulk_values.R
    
    813 Bytes
  - explore_analyzable_CpGs_RnBeads.R
    
    2.9 kB
  - find_closest_gene.R
    
    564 Bytes
- tapestri
  - 200804_Design_Mission_Bio_sites_Jurkat_K562.tsv
    
    27.8 kB
  - Blood.Bone.Marrow.Amplicons.design.dropout.added.selected.tsv
    
    128.8 kB
  - DoubletDetection.py
    
    615 Bytes
  - PG-135.csv
    
    66 Bytes
  - README.md
    
    1.7 kB
  - ab_adapters_3.fasta
    
    334 Bytes
  - ab_adapters_5.fasta
    
    26 Bytes
  - cellfinder.R
    
    1.6 kB
  - cellfinder_BCells.R
    
    1.4 kB
  - cellfinder_BCells_selected.R
    
    1.4 kB
  - config.yaml
    
    446 Bytes
  - panel.bed
    
    23.7 kB
  - rnbeads.yml
    
    16.7 kB
  - run_tapestri_BCells.sh
    
    643 Bytes
  - run_tapestri_BM.sh
    
    643 Bytes
  - run_tapestri_protein_BM.sh
    
    472 Bytes
  - run_tapestri_protein_Bcells.sh
    
    649 Bytes
  - tapestri_pipeline_BCells.sh
    
    5.5 kB
  - tapestri_pipeline_protein_BCells.sh
    
    1.8 kB
  - totalseq-d-heme-oncology-CD27.csv
    
    2.1 kB

scTAM-seq-scripts.zip