biosmoother
  • Quick Start
  • Overview
  • Taking a tour 🚌
    • Changing mapping quality filter
    • Zooming into a region of interest
    • Exporting a picture
  • Installation
    • Pip
    • Compiling Smoother yourself
    • Supported operating systems and browsers
  • Command organization
  • Creating an index
    • Initializing an index
    • Adding replicates to an index
      • Input format for the repl command
      • Preprocessing data for the repl command
        • Symmetric data sets, such as Hi-C or Micro-C
        • Asymmetric data sets, such as RD-SPRITE, or RADICL-seq
    • Adding tracks to an index
      • Input format for the track command
  • Using the graphical interface
    • Launching the graphical interface
      • Port forwarding on a server that uses slurm
      • Setting up a webserver with Smoother
    • Overview of Smoother’s interface
    • Navigation on Smoother
      • Plot tools
      • The Navigation bar
    • The Status bar
    • The File tab
      • The Presetting subtab
      • The Export subtab
      • The Info subtab
    • The Normalize tab
      • The Primary subtab
        • Binomial test normalization
        • Associated slices normalization
        • Iterative correction normalization
      • The Dist. Dep. Dec. subtab
      • The Ploidy subtab
        • Ploidy input format
    • The Filter tab
      • The Datapools subtab
      • The Mapping subtab
      • The Coordinates subtab
        • Annotation coordinate system
          • Prioritized annotation coordinate system
      • The Annotations subtab
    • The View tab
      • The Color subtab
      • The Panels subtab
      • The Bins subtab
      • The Virtual 4C subtab
      • The Rendering subtab
  • Using the command line interface
    • Correcting for ploidy
    • Setting parameters
    • Retrieving the values of parameters
    • Exporting pictures and data
    • Resetting an index
  • Citing Smoother
  • Appendix
    • Thanks
    • References
    • Version
  • Command line API reference
    • Positional Arguments
    • Named Arguments
    • Sub-commands
      • serve
        • Positional Arguments
        • Named Arguments
      • init
        • Positional Arguments
        • Named Arguments
      • reset
        • Positional Arguments
      • repl
        • Positional Arguments
        • Named Arguments
      • cool
        • Positional Arguments
        • Named Arguments
      • track
        • Positional Arguments
        • Named Arguments
      • export
        • Positional Arguments
        • Named Arguments
      • set
        • Positional Arguments
      • get
        • Positional Arguments
      • par_info
        • Positional Arguments
        • Named Arguments
      • test
        • Positional Arguments
        • Named Arguments
      • benchmark
        • Positional Arguments
        • Named Arguments
      • ploidy
        • Positional Arguments
    • Index Parameters
      • The Annotation group
        • filter_absent_x
        • filter_absent_y
        • filter_present_x
        • filter_present_y
        • visible_x
        • visible_y
        • area
      • The Contigs group
        • annotation_coordinates
        • displayed_on_x
        • displayed_on_x_ploidy
        • displayed_on_y
        • displayed_on_y_ploidy
      • The Coverage group
        • in_column
        • in_row
      • The Replicates group
        • in_group_a
        • in_group_b
      • The Settings group
        • The Export subgroup
          • axis
          • contigs
          • coords
          • do_export_full
          • export_format
          • export_to_server
          • margins
          • prefix
          • print_region
          • secondary_stroke_width
          • secondary_x_range
          • secondary_y_range
          • size
          • spacing
          • white_background
        • The Filters subgroup
          • ambiguous_mapping
          • anno_coords_col
          • anno_coords_row
          • anno_in_multiple_bins
          • cut_off_bin
          • directionality
          • incomplete_alignments
          • val_max
          • val_min
          • min_diag_dist
          • multiple_annos_in_bin
          • show_contig_smaller_than_bin
          • symmetry
        • The Interface subgroup
          • add_draw_area
          • anno_size
          • axis_label_max_char
          • axis_lables
          • center_tracks_on_bins
          • color_high
          • color_low
          • color_palette
          • connect_tracks_over_contig_borders
          • do_redraw
          • fixed_bin_size
          • fixed_bin_size_x
          • fixed_bin_size_y
          • fixed_num_bins_x
          • fixed_num_bins_y
          • fixed_number_of_bins
          • max_detailed_anno_display
          • max_num_bins
          • max_num_bins_factor
          • max_undo
          • min_bin_size
          • raw_size
          • annotation
          • axis
          • contig_borders
          • coords
          • grid_lines
          • heatmap
          • indent_line
          • raw
          • regs
          • tools
          • snap_bin_size
          • squared_bins
          • tracks_log_scale
          • update_freq
          • col
          • col_from
          • col_to
          • do_col
          • do_row
          • norm_by_viewpoint_size
          • row
          • row_from
          • row_to
          • zero_track_at_ends
          • zoom_redraw
        • The Normalization subgroup
          • color_range
          • ddd
          • ddd_all_samples
          • ddd_quantile
          • ddd_samples
          • ddd_show
          • grid_seq_annotation
          • grid_seq_axis_is_column
          • grid_seq_display_background
          • grid_seq_dna_filter_v2
          • grid_seq_filter_intersection
          • grid_seq_global
          • grid_seq_ignore_cis
          • grid_seq_max_bin_size
          • grid_seq_rna_filter_v2
          • grid_seq_samples
          • ice_ignore_n_diags
          • ice_local
          • ice_mad_max
          • ice_min_nz
          • ice_show_bias
          • ice_sparse_slice_filter
          • log_base
          • min_interactions
          • normalize_by
          • normalize_by_coverage
          • num_ice_bins
          • p_accept
          • ploidy_coords
          • ploidy_correct
          • ploidy_keep_distinct_group
          • ploidy_keep_inter_group
          • ploidy_remove_intra_instance_contig
          • ploidy_remove_others
          • radicl_local
          • radicl_seq_axis_is_column
          • radicl_seq_display_coverage
          • radicl_seq_samples
          • scale
        • The Replicates subgroup
          • between_group
          • in_group
  • Contents
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© Copyright 2023, Markus R. Schmidt, Anna Barcons-Simon, Claudia Rabuffo, and T. Nicolai Siegel.

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