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pycallingcards-tools
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  • Installation
  • Tutorials
    • Tutorial: Analyzing single cell calling cards collected from the mouse cortex
    • Tutorial: K562 HCT116 SP1 single-cell calling cards data.
    • Tutorial: Brd4 bindings for Male/Female mouse bulk calling cards data.
    • Tutorial: SP1 bindings in Cre-driver mouse lines.
    • Tutorial: Yeast TYE7 bulk calling cards data
  • User guide
  • API
    • Datasets
      • pycallingcards.datasets.mousecortex_data
      • pycallingcards.datasets.SP1_K562HCT116_data
      • pycallingcards.datasets.mouse_brd4_data
      • pycallingcards.datasets.SP1_Cre_data
    • Reading
      • pycallingcards.reading.read_qbed
      • pycallingcards.reading.read_rna
      • pycallingcards.reading.read_barbodes
      • pycallingcards.reading.combine_qbed
      • pycallingcards.reading.save_qbed
      • pycallingcards.reading.save_bed
    • Preprocessing
      • pycallingcards.preprocessing.clean_qbed
      • pycallingcards.preprocessing.call_peaks
      • pycallingcards.preprocessing.combine_peaks
      • pycallingcards.preprocessing.separate_peaks
      • pycallingcards.preprocessing.annotation
      • pycallingcards.preprocessing.make_Anndata
      • pycallingcards.preprocessing.filter_peaks
      • pycallingcards.preprocessing.adata_insertions
      • pycallingcards.preprocessing.down_sample
    • Tools
      • pycallingcards.tools.call_motif
      • pycallingcards.tools.compare_motif
      • pycallingcards.tools.rank_peak_groups
      • pycallingcards.tools.rank_peak_groups_mu
      • pycallingcards.tools.rank_peak_groups_df
      • pycallingcards.tools.diff2group_bygroup
      • pycallingcards.tools.diff2group_bysample
      • pycallingcards.tools.DE_pvalue
      • pycallingcards.tools.pair_peak_gene_bulk
      • pycallingcards.tools.pair_peak_gene_sc
      • pycallingcards.tools.pair_peak_gene_sc_mu
      • pycallingcards.tools.liftover
      • pycallingcards.tools.find_location
      • pycallingcards.tools.result_mapping
      • pycallingcards.tools.GWAS
      • pycallingcards.tools.GWAS_adata_bulk
      • pycallingcards.tools.GWAS_adata_sc
      • pycallingcards.tools.footprint
      • pycallingcards.tools.find_fastq
    • Plotting
      • pycallingcards.plotting.draw_area
      • pycallingcards.plotting.draw_area_mu
      • pycallingcards.plotting.whole_peaks
      • pycallingcards.plotting.calculate_signal
      • pycallingcards.plotting.signal_plot
      • pycallingcards.plotting.signal_heatmap
      • pycallingcards.plotting.rank_peak_groups
      • pycallingcards.plotting.plot_matched
      • pycallingcards.plotting.volcano_plot
      • pycallingcards.plotting.heatmap
      • pycallingcards.plotting.dotplot_bulk
      • pycallingcards.plotting.dotplot_sc
      • pycallingcards.plotting.dotplot_sc_mu
      • pycallingcards.plotting.WashU_browser_url
      • pycallingcards.plotting.GWAS_adata_sc
      • pycallingcards.plotting.GWAS_adata_bulk
  • Release notes
  • References
  • GitHub
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