Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | X | Y | Z A ABOUT (in module coalispr.tk_gui.gui_constants) ACOL (in module coalispr.resources.constant) add_widget() (coalispr.tk_gui.gui_widgets.opt.Options_frame method) (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame method) AEC (in module coalispr.resources.constant) Ago ALC (in module coalispr.resources.constant) ALL (in module coalispr.resources.constant) all_exps() (in module coalispr.bedgraph_analyze.experiment) ALPH (in module coalispr.resources.constant) anchored_text() (in module coalispr.resources.plot_utilities) ANNOTALPH (in module coalispr.resources.constant) annotate() (in module coalispr.coalispr) annotate_clust_file() (in module coalispr.count_analyze.annot) annotate_count_frame() (in module coalispr.count_analyze.annot) annotate_libtotals() (in module coalispr.count_analyze.annot) arg (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] args (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] args_dict (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] argvar (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] argvars (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] assemble_groupsamples() (in module coalispr.resources.dialog) AXCOL (in module coalispr.resources.constant) AXCOL2 (in module coalispr.resources.constant) AXLIMS (in module coalispr.resources.constant) B BACKEND (in module coalispr.resources.constant) background backup_pickle_to_tsv() (in module coalispr.bedgraph_analyze.store) BAK (in module coalispr.resources.constant) bam BAM (in module coalispr.resources.constant) BAM2BG (in module coalispr.resources.constant) BAM2BGNAM (in module coalispr.resources.constant) BamCounterController (class in coalispr.bedgraph_analyze.bam_counters) BAMHIGH (in module coalispr.resources.constant) BAMLOW (in module coalispr.resources.constant) BAMPEAK (in module coalispr.resources.constant) BamRegionCountController (class in coalispr.bedgraph_analyze.bam_counters) BAMSTART (in module coalispr.resources.constant) barcode barlinewidth (coalispr.count_analyze.panel_plotters.BrokenLengthPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.PanelPlotter attribute) barwidth (coalispr.count_analyze.panel_plotters.CountPanelPlotter attribute) BASEDIR (in module coalispr.resources.constant) bash BCKGRCOL (in module coalispr.resources.constant) BCO (in module coalispr.resources.constant) bedgraph BEDGRAPH (in module coalispr.resources.constant) bedgraphs_from_xtra_bamdata() (in module coalispr.bedgraph_analyze.process_bamdata) bgconvert_file() (in module coalispr.resources.share.convert_plusmin_bedgraph_to_plusplus) bin bin_bedgraphs() (in module coalispr.bedgraph_analyze.process_bedgraphs) binary numbers BinCounter (class in coalispr.bedgraph_analyze.bam_counters) BINN (in module coalispr.resources.constant) binners (coalispr.bedgraph_analyze.bam_counters.BamCounterController attribute) (coalispr.bedgraph_analyze.bam_counters.BamRegionCountController attribute) BinPanelPlotter (class in coalispr.count_analyze.panel_plotters) BINS (in module coalispr.resources.constant) bins_sum() (in module coalispr.resources.utilities) BINSTEP (in module coalispr.resources.constant) biological experiment biological replicate BIOR (in module coalispr.tk_gui.gui_constants) break_xaxis() (in module coalispr.resources.plot_utilities) BREG (in module coalispr.resources.constant) BrokenLengthPanelPlotter (class in coalispr.count_analyze.panel_plotters) C canvas_scroll_command() (coalispr.tk_gui.gui_widgets.opt.Options_frame method) canvas_scrollbar (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] capit_label() (in module coalispr.resources.plot_utilities) CAT_D (in module coalispr.resources.constant) CAT_M (in module coalispr.resources.constant) CAT_R (in module coalispr.resources.constant) CAT_S (in module coalispr.resources.constant) CAT_U (in module coalispr.resources.constant) CATEGORY (in module coalispr.resources.constant) cDNA change_subcommand() (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame method) chdir_current_exp() (in module coalispr.tk_gui.gui_utilities) checkset() (in module coalispr.bedgraph_analyze.collect_bedgraphs) checkSRCDIR() (in module coalispr.bedgraph_analyze.collect_bedgraphs) choice (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] choices (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame attribute), [1] choose_frame (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] chr_test() (in module coalispr.bedgraph_analyze.genom) chrnam (coalispr.bedgraph_analyze.genom.SegmentTrack attribute) (coalispr.bedgraph_analyze.genom.Track attribute), [1] chrno (coalispr.resources.share.ncfasta2gtf.Gtfline attribute), [1] chrom_region() (in module coalispr.resources.utilities) CHROMFIG (in module coalispr.resources.constant) CHROMLBL (in module coalispr.resources.constant) chroms() (in module coalispr.bedgraph_analyze.genom) CHRXTRA (in module coalispr.resources.constant) chrxtra() (in module coalispr.resources.utilities) cigar CIGARCHK (in module coalispr.resources.constant) CIGFM (in module coalispr.resources.constant) CIGPD (in module coalispr.resources.constant) CKEY1 (in module coalispr.resources.constant) CKEY2 (in module coalispr.resources.constant) CKEY3 (in module coalispr.resources.constant) CKEY4 (in module coalispr.resources.constant) clean_dict() (in module coalispr.resources.utilities) clean_fasta() (in module coalispr.resources.share.clean_fasta) clean_file() (in module coalispr.resources.share.no_empty_fa) clean_igb() (in module coalispr.resources.share.gtf_frm_tsv) CLI Cli_menu (class in coalispr.tk_gui.gui_widgets.cli) (class in coalispr.tk_gui.gui_widgets.menu_main) CLUSTGR (in module coalispr.resources.constant) CLUSTVIS (in module coalispr.resources.constant) CNTCDNA (in module coalispr.resources.constant) CNTGAP (in module coalispr.resources.constant) CNTLABELS (in module coalispr.resources.constant) cntlabl (coalispr.bedgraph_analyze.bam_counters.LengthCounter attribute) (coalispr.bedgraph_analyze.bam_counters.MultiMapCounter attribute) (coalispr.bedgraph_analyze.bam_counters.RegionLengthCounter attribute), [1] CNTREAD (in module coalispr.resources.constant) CNTRS (in module coalispr.resources.constant) CNTSKIP (in module coalispr.resources.constant) coalispr module coalispr() (in module coalispr.coalispr) coalispr.__main__ module coalispr.bedgraph_analyze module coalispr.bedgraph_analyze.bam_counters module coalispr.bedgraph_analyze.bedgraph_plots module coalispr.bedgraph_analyze.collect_bedgraphs module coalispr.bedgraph_analyze.compare module coalispr.bedgraph_analyze.experiment module coalispr.bedgraph_analyze.genom module coalispr.bedgraph_analyze.info_plots module coalispr.bedgraph_analyze.process_bamdata module coalispr.bedgraph_analyze.process_bedgraphs module coalispr.bedgraph_analyze.references module coalispr.bedgraph_analyze.store module coalispr.bedgraph_analyze.unselected module coalispr.coalispr module coalispr.count_analyze module coalispr.count_analyze.annot module coalispr.count_analyze.countfile_plots module coalispr.count_analyze.filter_data module coalispr.count_analyze.groupcompare_plots module coalispr.count_analyze.load_countfile module coalispr.count_analyze.panel_plotters module coalispr.count_analyze.regioncount_plots module coalispr.resources module coalispr.resources.cmd_parser module coalispr.resources.constant module coalispr.resources.constant_in module coalispr.resources.constant_in.make_constant module coalispr.resources.dialog module coalispr.resources.numeric module coalispr.resources.plot_utilities module coalispr.resources.profilehooks module coalispr.resources.share module coalispr.resources.share.clean_fasta module coalispr.resources.share.cols_from_csv_to_tab module coalispr.resources.share.convert_gff3 module coalispr.resources.share.convert_plusmin_bedgraph_to_plusplus module coalispr.resources.share.genbank2gtf module coalispr.resources.share.get_smallRNAs_and_targets module coalispr.resources.share.gtf_frm_tsv module coalispr.resources.share.ncfasta2gtf module coalispr.resources.share.no_empty_fa module coalispr.resources.share.reduce_gtf module coalispr.resources.share.revseq module coalispr.resources.share.sub_gtf module coalispr.resources.utilities module coalispr.tk_gui module coalispr.tk_gui.customtkinter module coalispr.tk_gui.customtkinter.font_manager module coalispr.tk_gui.gui_constants module coalispr.tk_gui.gui_utilities module coalispr.tk_gui.gui_widgets module coalispr.tk_gui.gui_widgets.cli module coalispr.tk_gui.gui_widgets.menu_main module coalispr.tk_gui.gui_widgets.opt module coalispr.tk_gui.gui_widgets.opt2 module coalispr.tk_gui.tk_coalispr module Coalispr_app (class in coalispr.tk_gui.tk_coalispr) collapsed COLLAPSED (in module coalispr.resources.constant) collect_bamfiles() (in module coalispr.bedgraph_analyze.process_bamdata) collect_bedgraphs() (in module coalispr.bedgraph_analyze.collect_bedgraphs) collect_coseqframes() (in module coalispr.count_analyze.filter_data) collect_limits() (in module coalispr.resources.dialog) collect_references() (in module coalispr.bedgraph_analyze.collect_bedgraphs) COLLR (in module coalispr.resources.constant) colr (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] COLS (in module coalispr.bedgraph_analyze.bam_counters) COMBI (in module coalispr.resources.constant) comm_description (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] command (coalispr.tk_gui.gui_widgets.cli.Command_frames attribute) (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] COMMAND_DESCRIPTIONS (in module coalispr.tk_gui.gui_constants) command_field (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] command_frame (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] Command_frames (class in coalispr.tk_gui.gui_widgets.cli) (class in coalispr.tk_gui.gui_widgets.menu_main) command_frames (coalispr.tk_gui.gui_widgets.cli.Command_frames attribute) (coalispr.tk_gui.gui_widgets.menu_main.Command_frames attribute) command_submit (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] command_var (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] COMMANDS (in module coalispr.tk_gui.gui_constants) compare_5nt_lengths() (in module coalispr.count_analyze.groupcompare_plots) compare_exp_bins() (in module coalispr.count_analyze.countfile_plots) compare_exp_lengths() (in module coalispr.count_analyze.countfile_plots) compare_exp_mulmaps() (in module coalispr.count_analyze.countfile_plots) compare_libtotals() (in module coalispr.count_analyze.countfile_plots) compare_un_spec_lengths() (in module coalispr.count_analyze.countfile_plots) compare_un_spec_mulmaps() (in module coalispr.count_analyze.countfile_plots) comparereads (coalispr.bedgraph_analyze.bam_counters.BamRegionCountController attribute) CONDITION (in module coalispr.resources.constant) CONDITIONS (in module coalispr.resources.constant), [1] CONFBASE (in module coalispr.resources.constant) CONFFILE (in module coalispr.resources.constant) CONFFOLDER (in module coalispr.resources.constant) CONFIG (in module coalispr.resources.constant) config_from_newdirs() (in module coalispr.bedgraph_analyze.store) CONFNAM (in module coalispr.resources.constant) CONFPATH (in module coalispr.resources.constant) constant CONSTANT (in module coalispr.resources.constant) CONTEXT (in module coalispr.resources.constant) controls() (in module coalispr.bedgraph_analyze.experiment) convert_gff() (in module coalispr.resources.share.convert_gff3) convtab (in module coalispr.resources.share.genbank2gtf) CORB (in module coalispr.resources.constant) corb_keycntr (coalispr.bedgraph_analyze.bam_counters.LengthCounter attribute) corbett COSEQ (in module coalispr.resources.constant) COU (in module coalispr.resources.constant) count_folder() (in module coalispr.bedgraph_analyze.process_bamdata) count_frame() (in module coalispr.bedgraph_analyze.bam_counters) countbams() (in module coalispr.coalispr) Counter (class in coalispr.bedgraph_analyze.bam_counters) CountPanelPlotter (class in coalispr.count_analyze.panel_plotters) coverage coverage() (in module coalispr.resources.profilehooks) CPPHFAC (in module coalispr.resources.constant) create_checkbtn() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) create_combo() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) create_comboE() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) create_entry() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) create_entry2() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) create_genom_indexes() (in module coalispr.bedgraph_analyze.genom) create_gtf() (in module coalispr.resources.share.sub_gtf) create_gtfs() (in module coalispr.resources.share.get_smallRNAs_and_targets) create_helpframe() (coalispr.tk_gui.gui_widgets.cli.Main_frame method) (coalispr.tk_gui.gui_widgets.menu_main.Main_frame method) create_init_frame() (coalispr.tk_gui.gui_widgets.cli.Command_frames method) create_init_panel() (coalispr.tk_gui.gui_widgets.opt.Options_frame method) create_prog_frame() (coalispr.tk_gui.gui_widgets.cli.Command_frames method) (coalispr.tk_gui.gui_widgets.menu_main.Command_frames method) create_runframe() (coalispr.tk_gui.gui_widgets.cli.Main_frame method) (coalispr.tk_gui.gui_widgets.menu_main.Main_frame method) create_siRNA_GTF_line() (in module coalispr.resources.share.gtf_frm_tsv) CSFONTSZ (in module coalispr.resources.constant) csv current_widget (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame attribute), [1] custom_theme (coalispr.tk_gui.tk_coalispr.Coalispr_app attribute) CVAL1 (in module coalispr.resources.constant) CVAL2 (in module coalispr.resources.constant) CVAL3 (in module coalispr.resources.constant) CVAL4 (in module coalispr.resources.constant) CWD (in module coalispr.resources.constant) CYTO (in module coalispr.resources.constant) D DARKTHEME (in module coalispr.resources.constant) DATA (in module coalispr.resources.constant) DATASTOR (in module coalispr.resources.constant) DCOL (in module coalispr.resources.constant) DEFAULT_EMPTY_VALUE (in module coalispr.tk_gui.gui_constants) default_value (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] DENSE (in module coalispr.resources.constant) depletion kits DESCRIPTION (coalispr.tk_gui.gui_widgets.cli.Main_frame attribute) (coalispr.tk_gui.gui_widgets.menu_main.Main_frame attribute) (in module coalispr.resources.constant) descriptions (coalispr.tk_gui.gui_widgets.cli.Command_frames attribute) DETECTTHEME (in module coalispr.resources.constant) df (coalispr.bedgraph_analyze.genom.SegmentTrack attribute), [1] (coalispr.bedgraph_analyze.genom.Track attribute), [1] (coalispr.count_analyze.panel_plotters.BinPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.BrokenLengthPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1] discard DISCARD (in module coalispr.resources.constant) discarded() (in module coalispr.bedgraph_analyze.experiment) display_choices() (coalispr.resources.dialog.PresentDialog method) display_dialog() (coalispr.resources.dialog.PresentDialog method) DNAXTRA (in module coalispr.resources.constant) DNAXTRNAM (in module coalispr.resources.constant) DOCU (in module coalispr.tk_gui.gui_constants) dolegend (coalispr.count_analyze.panel_plotters.BinPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.BrokenLengthPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.LengthPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1] doneon() (in module coalispr.resources.utilities) DPI (in module coalispr.resources.constant) drop_discarded() (in module coalispr.bedgraph_analyze.experiment) dtype (coalispr.bedgraph_analyze.bam_counters.BinCounter attribute) (coalispr.bedgraph_analyze.bam_counters.Counter attribute) (coalispr.bedgraph_analyze.bam_counters.LengthCounter attribute) (coalispr.bedgraph_analyze.bam_counters.RegionLengthCounter attribute) (coalispr.bedgraph_analyze.bam_counters.SkipCounter attribute) DWNLDS (in module coalispr.resources.constant) E edit_toolbar() (in module coalispr.resources.plot_utilities) enabled (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] encoding (in module coalispr.bedgraph_analyze.compare) ENDRET (in module coalispr.resources.constant) epitope equals() (coalispr.resources.share.ncfasta2gtf.Gtfline method) errortext (coalispr.resources.dialog.PresentDialog attribute) EXCELL (in module coalispr.resources.constant) exclusive_arg_options (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] EXP (in module coalispr.resources.constant) EXPDISP (in module coalispr.resources.constant) EXPERIMENT (in module coalispr.resources.constant) EXPFILE (in module coalispr.resources.constant) EXPFILNAM (in module coalispr.resources.constant) EXPNAM (in module coalispr.resources.constant) EXPTXT (in module coalispr.resources.constant) extra exts (in module coalispr.resources.share.genbank2gtf) (in module coalispr.resources.share.gtf_frm_tsv) (in module coalispr.resources.share.ncfasta2gtf) F fasta FASTA (in module coalispr.resources.constant) fasta2gtf() (in module coalispr.resources.share.ncfasta2gtf) fastq fcie (coalispr.count_analyze.panel_plotters.BrokenLengthPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.CountPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.LengthPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.Log2CountPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.Log2RegionCountPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.RegionCountPanelPlotter attribute) (coalispr.resources.dialog.PresentDialog attribute), [1] FIELDFONTSIZE (in module coalispr.tk_gui.gui_constants) fig (coalispr.count_analyze.panel_plotters.PanelPlotter attribute) FIGCOL (in module coalispr.resources.constant) FIGDIR (in module coalispr.resources.constant) FIGDIRJPG (in module coalispr.resources.constant) FIGDIRPDF (in module coalispr.resources.constant) FIGDIRPNG (in module coalispr.resources.constant) FIGDIRSVG (in module coalispr.resources.constant) FIGFORMAT (in module coalispr.resources.constant) FIGS (in module coalispr.resources.constant) figure (coalispr.count_analyze.panel_plotters.PanelPlotter attribute) FIGXLABEL (in module coalispr.resources.constant) FIGYLABEL (in module coalispr.resources.constant) FILEKEY (in module coalispr.resources.constant) filter_negative_from_reference() (in module coalispr.bedgraph_analyze.process_bedgraphs) filtered_referencetrack() (in module coalispr.bedgraph_analyze.references) Float64Index (class in coalispr.resources.numeric) FontManager (class in coalispr.tk_gui.customtkinter.font_manager) for_group() (in module coalispr.bedgraph_analyze.experiment) format_ax (coalispr.count_analyze.panel_plotters.BrokenLengthPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.LengthPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.PanelPlotter attribute) FRACTION (in module coalispr.resources.constant) FRACTIONS (in module coalispr.resources.constant) G gap (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1] gather_all_specific_regions() (in module coalispr.bedgraph_analyze.compare) gather_all_unspecific_regions() (in module coalispr.bedgraph_analyze.compare) genbank2gtf() (in module coalispr.resources.share.genbank2gtf) gentype (coalispr.resources.share.ncfasta2gtf.Gtfline attribute), [1] get_available_fonts() (in module coalispr.tk_gui.gui_utilities) get_categories_dict() (in module coalispr.bedgraph_analyze.collect_bedgraphs) get_coalispr_theme() (in module coalispr.tk_gui.gui_utilities) get_cols() (in module coalispr.bedgraph_analyze.bam_counters) get_commands() (in module coalispr.coalispr) get_context() (in module coalispr.resources.plot_utilities) get_count_frame() (coalispr.bedgraph_analyze.bam_counters.RegionLengthCounter method) (coalispr.bedgraph_analyze.bam_counters.SkipCounter method) get_count_frames() (coalispr.bedgraph_analyze.bam_counters.BamRegionCountController method) get_ctext() (coalispr.bedgraph_analyze.genom.Track method) get_descriptions() (in module coalispr.resources.cmd_parser) get_discard() (in module coalispr.bedgraph_analyze.experiment) get_experiment_name() (in module coalispr.resources.dialog) get_experiments() (in module coalispr.bedgraph_analyze.collect_bedgraphs) get_freq_frame() (in module coalispr.count_analyze.load_countfile) get_genom_indexes() (in module coalispr.bedgraph_analyze.genom) get_grplabels() (in module coalispr.bedgraph_analyze.experiment) get_GTF_comment() (in module coalispr.resources.share.gtf_frm_tsv) get_indexes() (in module coalispr.bedgraph_analyze.compare) get_input_widget() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) get_inputtotals() (in module coalispr.bedgraph_analyze.store) get_lencount_frame() (coalispr.bedgraph_analyze.bam_counters.RegionLengthCounter method) (coalispr.bedgraph_analyze.bam_counters.SkipCounter method) get_lencount_frames() (coalispr.bedgraph_analyze.bam_counters.BamRegionCountController method) get_lengths() (in module coalispr.bedgraph_analyze.genom) get_mutant() (in module coalispr.bedgraph_analyze.experiment) get_negative() (in module coalispr.bedgraph_analyze.experiment) get_old_new_samplenames() (in module coalispr.resources.dialog) get_parser() (in module coalispr.coalispr) get_picks() (in module coalispr.bedgraph_analyze.experiment) get_positive() (in module coalispr.bedgraph_analyze.experiment) get_readlengths_frame() (in module coalispr.count_analyze.load_countfile) get_reference() (in module coalispr.bedgraph_analyze.experiment) get_region_pattern() (in module coalispr.resources.dialog) get_segments() (coalispr.bedgraph_analyze.genom.Track method) get_skip() (in module coalispr.resources.utilities) get_string_info() (in module coalispr.resources.utilities) get_tsvpath() (in module coalispr.resources.utilities) get_unselected_folderpath() (in module coalispr.bedgraph_analyze.store) get_version() (in module coalispr.coalispr) get_ylabel() (in module coalispr.resources.utilities) goption() (in module coalispr.bedgraph_analyze.experiment) GRANUL (in module coalispr.resources.constant) GRID (in module coalispr.resources.constant) grid_column (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame attribute), [1] GRIDALPHA (in module coalispr.resources.constant) GRIDAXIS (in module coalispr.resources.constant) GRIDCOLOR (in module coalispr.resources.constant) GRIDSTYLE (in module coalispr.resources.constant) GRIDWHICH (in module coalispr.resources.constant) group (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1] GROUP (in module coalispr.resources.constant) GROUPAVG (in module coalispr.resources.constant) groupcompare() (in module coalispr.coalispr) GTF GTFEXON (in module coalispr.resources.constant) GTFFEAT (in module coalispr.resources.constant) Gtfline (class in coalispr.resources.share.ncfasta2gtf) GTFREF (in module coalispr.resources.constant) GTFREFNAM (in module coalispr.resources.constant) GTFS (in module coalispr.resources.constant) GTFSPEC (in module coalispr.resources.constant) GTFSPECNAM (in module coalispr.resources.constant) GTFtrack (class in coalispr.bedgraph_analyze.genom) GTFUNSP (in module coalispr.resources.constant) GTFUNSPNAM (in module coalispr.resources.constant) GTFUNXTNAM (in module coalispr.resources.constant) GTFUNXTR (in module coalispr.resources.constant) GTFXTRA (in module coalispr.resources.constant) GTFXTRANAM (in module coalispr.resources.constant) GUI H h99 (in module coalispr.resources.share.cols_from_csv_to_tab) h_tab (coalispr.tk_gui.gui_widgets.cli.Main_frame attribute) (coalispr.tk_gui.gui_widgets.menu_main.Main_frame attribute) handle (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] has_been_counted() (in module coalispr.bedgraph_analyze.process_bamdata) has_discards() (in module coalispr.bedgraph_analyze.experiment) has_grouparg() (in module coalispr.bedgraph_analyze.experiment) has_redundant_muts() (in module coalispr.bedgraph_analyze.experiment) has_unselected() (in module coalispr.bedgraph_analyze.unselected) headers (in module coalispr.resources.share.gtf_frm_tsv) HELP (coalispr.tk_gui.gui_widgets.cli.Main_frame attribute) (coalispr.tk_gui.gui_widgets.menu_main.Main_frame attribute) hfac (coalispr.count_analyze.panel_plotters.LengthPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1] (coalispr.count_analyze.panel_plotters.RegionCountPanelPlotter attribute) HI (in module coalispr.resources.constant) HIGHALPH (in module coalispr.resources.constant) HIGHLEG (in module coalispr.resources.constant) HIGHLINEW (in module coalispr.resources.constant) hold_frame (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] HOME (in module coalispr.resources.constant) I idxnam (coalispr.bedgraph_analyze.bam_counters.LengthCounter attribute) (coalispr.bedgraph_analyze.bam_counters.MultiMapCounter attribute) (coalispr.bedgraph_analyze.bam_counters.RegionLengthCounter attribute), [1] immunoprecipitation in_venv() (in module coalispr.coalispr) INACTIVATE (in module coalispr.tk_gui.gui_constants) include_test() (in module coalispr.resources.cmd_parser) INFO (in module coalispr.tk_gui.gui_constants) info() (in module coalispr.coalispr) INFOREGS (in module coalispr.resources.constant) init() (in module coalispr.coalispr) init_font_manager() (coalispr.tk_gui.customtkinter.font_manager.FontManager class method) init_frame (coalispr.tk_gui.gui_widgets.cli.Command_frames attribute) init_panel (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute) init_sns() (in module coalispr.resources.plot_utilities) INMAPCOLL (in module coalispr.resources.constant) INMAPUNCOLL (in module coalispr.resources.constant) input (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] INPUTRCS (in module coalispr.resources.constant) Int64Index (class in coalispr.resources.numeric) IntegerIndex (class in coalispr.resources.numeric) INTR (in module coalispr.resources.constant) INTSTEP (in module coalispr.resources.constant) IP is_all_zero() (in module coalispr.resources.utilities) is_one_of_list() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) is_one_of_list_ (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] item (coalispr.resources.dialog.PresentDialog attribute), [1] J jec21 (in module coalispr.resources.share.cols_from_csv_to_tab) joinall() (in module coalispr.resources.utilities) joiner() (in module coalispr.resources.utilities) JPG (in module coalispr.resources.constant) K key (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute) keycntr (coalispr.bedgraph_analyze.bam_counters.RegionLengthCounter attribute) keys_counted_libs() (in module coalispr.bedgraph_analyze.process_bamdata) kind (coalispr.bedgraph_analyze.genom.GTFtrack attribute), [1] L label (coalispr.bedgraph_analyze.bam_counters.Counter attribute), [1] label0 (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] label1 (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] label_frame() (in module coalispr.bedgraph_analyze.collect_bedgraphs) labframe (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame attribute), [1] LEGNCOL (in module coalispr.resources.constant) LEN (in module coalispr.resources.constant) LENCDNA (in module coalispr.resources.constant) LENCNTRS (in module coalispr.resources.constant) LENCNTS (in module coalispr.resources.constant) LENCOUNTS (in module coalispr.resources.constant) LENGAP (in module coalispr.resources.constant) LengthCounter (class in coalispr.bedgraph_analyze.bam_counters) LengthPanelPlotter (class in coalispr.count_analyze.panel_plotters) LENGTHSFILE (in module coalispr.resources.constant) LENGTHSNAM (in module coalispr.resources.constant) LENMER (in module coalispr.resources.constant) LENREAD (in module coalispr.resources.constant) lens (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1] LENXTRA (in module coalispr.resources.constant) LENXTRAFILE (in module coalispr.resources.constant) LENXTRFILNAM (in module coalispr.resources.constant) less_xlabels() (in module coalispr.resources.plot_utilities) LIBCNTS (in module coalispr.resources.constant) LIBR (in module coalispr.resources.constant) lineobjects (coalispr.resources.share.ncfasta2gtf.Gtfline attribute) LINEW (in module coalispr.resources.constant) LINLIM (in module coalispr.resources.constant) linux_font_path (coalispr.tk_gui.customtkinter.font_manager.FontManager attribute) load_bin_table_perc() (in module coalispr.count_analyze.load_countfile) load_command() (coalispr.tk_gui.gui_widgets.cli.Cli_menu method) (coalispr.tk_gui.gui_widgets.menu_main.Cli_menu method) load_count_table() (in module coalispr.count_analyze.load_countfile) load_file() (in module coalispr.resources.share.cols_from_csv_to_tab) load_font() (coalispr.tk_gui.customtkinter.font_manager.FontManager class method) load_lengths_table_perc() (in module coalispr.count_analyze.load_countfile) load_list() (in module coalispr.resources.share.cols_from_csv_to_tab) log2_ax (coalispr.count_analyze.panel_plotters.CountPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.Log2CountPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.Log2RegionCountPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.RegionCountPanelPlotter attribute) LOG2BG (in module coalispr.resources.constant) LOG2BGTST (in module coalispr.resources.constant) Log2CountPanelPlotter (class in coalispr.count_analyze.panel_plotters) Log2RegionCountPanelPlotter (class in coalispr.count_analyze.panel_plotters) LOGFIL (in module coalispr.resources.constant) LOGFILNAM (in module coalispr.resources.constant) logger (in module coalispr.bedgraph_analyze.bam_counters) (in module coalispr.bedgraph_analyze.bedgraph_plots) (in module coalispr.bedgraph_analyze.collect_bedgraphs) (in module coalispr.bedgraph_analyze.compare) (in module coalispr.bedgraph_analyze.genom) (in module coalispr.bedgraph_analyze.info_plots) (in module coalispr.bedgraph_analyze.process_bamdata) (in module coalispr.bedgraph_analyze.process_bedgraphs) (in module coalispr.bedgraph_analyze.references) (in module coalispr.bedgraph_analyze.store) (in module coalispr.bedgraph_analyze.unselected) (in module coalispr.count_analyze.annot) (in module coalispr.count_analyze.countfile_plots) (in module coalispr.count_analyze.groupcompare_plots) (in module coalispr.count_analyze.load_countfile) (in module coalispr.count_analyze.panel_plotters) (in module coalispr.count_analyze.regioncount_plots) (in module coalispr.resources.constant_in.make_constant) (in module coalispr.resources.dialog) (in module coalispr.resources.plot_utilities) (in module coalispr.resources.utilities) (in module coalispr.tk_gui.gui_utilities) (in module coalispr.tk_gui.gui_widgets.menu_main) (in module coalispr.tk_gui.tk_coalispr) LOGLIM (in module coalispr.resources.constant) LOGMAX (in module coalispr.resources.constant) LOGO (in module coalispr.tk_gui.gui_constants) LOGS (in module coalispr.resources.constant) LOWLEG (in module coalispr.resources.constant) LOWR (in module coalispr.resources.constant) LPPHFAC (in module coalispr.resources.constant) LWIDTH (in module coalispr.tk_gui.gui_constants) M main (coalispr.tk_gui.gui_widgets.cli.Cli_menu attribute) (coalispr.tk_gui.tk_coalispr.Coalispr_app attribute) main() (in module coalispr.coalispr) (in module coalispr.resources.constant_in.make_constant) (in module coalispr.resources.share.clean_fasta) (in module coalispr.resources.share.cols_from_csv_to_tab) (in module coalispr.resources.share.convert_gff3) (in module coalispr.resources.share.convert_plusmin_bedgraph_to_plusplus) (in module coalispr.resources.share.genbank2gtf) (in module coalispr.resources.share.get_smallRNAs_and_targets) (in module coalispr.resources.share.gtf_frm_tsv) (in module coalispr.resources.share.ncfasta2gtf) (in module coalispr.resources.share.no_empty_fa) (in module coalispr.resources.share.reduce_gtf) (in module coalispr.resources.share.revseq) (in module coalispr.resources.share.sub_gtf) (in module coalispr.tk_gui.tk_coalispr) Main_frame (class in coalispr.tk_gui.gui_widgets.cli) (class in coalispr.tk_gui.gui_widgets.menu_main) make_constant() (in module coalispr.resources.constant_in.make_constant) make_parser() (in module coalispr.resources.cmd_parser) master (coalispr.tk_gui.gui_widgets.cli.Command_frames attribute) (coalispr.tk_gui.gui_widgets.menu_main.Command_frames attribute) (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] MAXGAP (in module coalispr.resources.constant) MAXMM (in module coalispr.resources.constant) MAXROW (in module coalispr.resources.constant) MCOL (in module coalispr.resources.constant) MEAN (in module coalispr.resources.constant) MEDIAN (in module coalispr.resources.constant) MEMBR (in module coalispr.resources.constant) menu (coalispr.tk_gui.tk_coalispr.Coalispr_app attribute) MENUFONTSIZE (in module coalispr.tk_gui.gui_constants) merg() (in module coalispr.resources.utilities) merge_lencounters() (coalispr.bedgraph_analyze.bam_counters.BamCounterController method) (coalispr.bedgraph_analyze.bam_counters.BamRegionCountController method) (coalispr.bedgraph_analyze.bam_counters.Counter method) (coalispr.bedgraph_analyze.bam_counters.LengthCounter method) (coalispr.bedgraph_analyze.bam_counters.RegionLengthCounter method) merge_reference() (in module coalispr.bedgraph_analyze.process_bedgraphs) merge_sets() (in module coalispr.bedgraph_analyze.process_bedgraphs) merge_unsel() (in module coalispr.bedgraph_analyze.unselected) METHCOL (in module coalispr.resources.constant) METHOD (in module coalispr.resources.constant) METHODS (in module coalispr.resources.constant) MI (in module coalispr.resources.constant) MINGAP (in module coalispr.resources.constant) MININTRON (in module coalispr.resources.constant) MINUS (in module coalispr.resources.constant) MINUSIN (in module coalispr.resources.constant) miRNA MIRNAPKBUF (in module coalispr.resources.constant) MITOCH (in module coalispr.resources.constant) mixed_groups() (in module coalispr.bedgraph_analyze.experiment) MMAPCNTRS (in module coalispr.resources.constant) mmappers (coalispr.bedgraph_analyze.bam_counters.BamCounterController attribute) (coalispr.bedgraph_analyze.bam_counters.BamRegionCountController attribute) module coalispr coalispr.__main__ coalispr.bedgraph_analyze coalispr.bedgraph_analyze.bam_counters coalispr.bedgraph_analyze.bedgraph_plots coalispr.bedgraph_analyze.collect_bedgraphs coalispr.bedgraph_analyze.compare coalispr.bedgraph_analyze.experiment coalispr.bedgraph_analyze.genom coalispr.bedgraph_analyze.info_plots coalispr.bedgraph_analyze.process_bamdata coalispr.bedgraph_analyze.process_bedgraphs coalispr.bedgraph_analyze.references coalispr.bedgraph_analyze.store coalispr.bedgraph_analyze.unselected coalispr.coalispr coalispr.count_analyze coalispr.count_analyze.annot coalispr.count_analyze.countfile_plots coalispr.count_analyze.filter_data coalispr.count_analyze.groupcompare_plots coalispr.count_analyze.load_countfile coalispr.count_analyze.panel_plotters coalispr.count_analyze.regioncount_plots coalispr.resources coalispr.resources.cmd_parser coalispr.resources.constant coalispr.resources.constant_in coalispr.resources.constant_in.make_constant coalispr.resources.dialog coalispr.resources.numeric coalispr.resources.plot_utilities coalispr.resources.profilehooks coalispr.resources.share coalispr.resources.share.clean_fasta coalispr.resources.share.cols_from_csv_to_tab coalispr.resources.share.convert_gff3 coalispr.resources.share.convert_plusmin_bedgraph_to_plusplus coalispr.resources.share.genbank2gtf coalispr.resources.share.get_smallRNAs_and_targets coalispr.resources.share.gtf_frm_tsv coalispr.resources.share.ncfasta2gtf coalispr.resources.share.no_empty_fa coalispr.resources.share.reduce_gtf coalispr.resources.share.revseq coalispr.resources.share.sub_gtf coalispr.resources.utilities coalispr.tk_gui coalispr.tk_gui.customtkinter coalispr.tk_gui.customtkinter.font_manager coalispr.tk_gui.gui_constants coalispr.tk_gui.gui_utilities coalispr.tk_gui.gui_widgets coalispr.tk_gui.gui_widgets.cli coalispr.tk_gui.gui_widgets.menu_main coalispr.tk_gui.gui_widgets.opt coalispr.tk_gui.gui_widgets.opt2 coalispr.tk_gui.tk_coalispr mouse (in module coalispr.resources.share.cols_from_csv_to_tab) MPLDEBUG (in module coalispr.resources.constant) mRNA msg (coalispr.resources.dialog.PresentDialog attribute) msg1 (coalispr.resources.dialog.PresentDialog attribute) msg2 (coalispr.resources.dialog.PresentDialog attribute) MULMAP (in module coalispr.resources.constant) MULMAPCOLL (in module coalispr.resources.constant) MULMAPUNCOLL (in module coalispr.resources.constant) MultiMapCounter (class in coalispr.bedgraph_analyze.bam_counters) multimapper MUNR (in module coalispr.resources.constant) munr_keycntr (coalispr.bedgraph_analyze.bam_counters.LengthCounter attribute) munro mutant MUTANT (in module coalispr.resources.constant) mutant() (in module coalispr.bedgraph_analyze.experiment) mutant_groups() (in module coalispr.bedgraph_analyze.experiment) MUTANTS (in module coalispr.resources.constant) MUTGROUPS (in module coalispr.resources.constant) MUTNO (in module coalispr.resources.constant) N name (in module coalispr) (in module coalispr.bedgraph_analyze) (in module coalispr.count_analyze) (in module coalispr.resources) (in module coalispr.resources.constant_in) (in module coalispr.resources.share) (in module coalispr.tk_gui) (in module coalispr.tk_gui.customtkinter) (in module coalispr.tk_gui.gui_widgets) nams (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1] NCOL (in module coalispr.resources.constant) negative control negative() (in module coalispr.bedgraph_analyze.experiment) NEGCTL (in module coalispr.resources.constant) NH (in module coalispr.resources.constant) NM (in module coalispr.resources.constant) NMD no_titles() (in module coalispr.resources.plot_utilities) NOCHOICE (in module coalispr.resources.constant) noise NONCAPT (in module coalispr.resources.constant) not_keycntr (coalispr.bedgraph_analyze.bam_counters.SkipCounter attribute) NOTAGIP (in module coalispr.resources.constant) notcount (coalispr.bedgraph_analyze.bam_counters.SkipCounter attribute) notfram (coalispr.bedgraph_analyze.bam_counters.SkipCounter attribute) NRMISM (in module coalispr.resources.constant) nt NUCL (in module coalispr.resources.constant) NUCLEO (in module coalispr.resources.constant) num_counted_libs() (in module coalispr.bedgraph_analyze.process_bamdata) numbers (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1] NumericIndex (class in coalispr.resources.numeric) O on_closing() (coalispr.tk_gui.tk_coalispr.Coalispr_app method) on_invalid() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) one_of_destinations (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] open_cmd (coalispr.tk_gui.tk_coalispr.Coalispr_app attribute) Option_widget (class in coalispr.tk_gui.gui_widgets.opt2) Options_frame (class in coalispr.tk_gui.gui_widgets.opt) OTHR (in module coalispr.resources.constant) othr() (in module coalispr.bedgraph_analyze.experiment) OUTPATH (in module coalispr.resources.constant) OUTPUTS (in module coalispr.resources.constant) P p (in module coalispr.resources.constant) (in module coalispr.tk_gui.gui_constants) (in module coalispr.tk_gui.gui_utilities) (in module coalispr.tk_gui.tk_coalispr) P2TDELIM (in module coalispr.resources.constant) PALETTE (in module coalispr.resources.constant) PanelPlotter (class in coalispr.count_analyze.panel_plotters) parent (coalispr.tk_gui.gui_widgets.menu_main.Cli_menu attribute), [1] (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] parse_open() (in module coalispr.tk_gui.tk_coalispr) pattern (coalispr.resources.dialog.PresentDialog attribute), [1] PCKG (in module coalispr.tk_gui.gui_constants) PCR PDF (in module coalispr.resources.constant) PE per_confirm (coalispr.resources.dialog.PresentDialog attribute), [1] PERC (in module coalispr.resources.constant) percentaged() (in module coalispr.resources.utilities) pickle_from_backup_tsv() (in module coalispr.bedgraph_analyze.store) pkl PKL2TSV (in module coalispr.resources.constant) PL (in module coalispr.resources.constant) plot_chrset() (in module coalispr.bedgraph_analyze.bedgraph_plots) plot_panels() (coalispr.count_analyze.panel_plotters.PanelPlotter method) plot_regioncounts() (in module coalispr.count_analyze.regioncount_plots) plot_regionlengths() (in module coalispr.count_analyze.regioncount_plots) PLOTALL (in module coalispr.resources.constant) PLOTFREQ (in module coalispr.resources.constant) PLOTINTRLEN (in module coalispr.resources.constant) PLOTLEN (in module coalispr.resources.constant) PLOTLIB (in module coalispr.resources.constant) PLOTMEAN (in module coalispr.resources.constant) PLOTMEDIAN (in module coalispr.resources.constant) PLOTMMAP (in module coalispr.resources.constant) PLOTPERC (in module coalispr.resources.constant) PLOTRAW (in module coalispr.resources.constant) PLOTSPEC (in module coalispr.resources.constant) PLOTSTRT (in module coalispr.resources.constant) PLOTUNSP (in module coalispr.resources.constant) PLUS (in module coalispr.resources.constant) PLUSIN (in module coalispr.resources.constant) png PNG (in module coalispr.resources.constant) POSCTL (in module coalispr.resources.constant) positive control positive() (in module coalispr.bedgraph_analyze.experiment) posslabels (in module coalispr.count_analyze.regioncount_plots) prefix (in module coalispr.resources.share.gtf_frm_tsv) PresentDialog (class in coalispr.resources.dialog) PRGNAM (in module coalispr.resources.constant) print_memory_usage_merged() (in module coalispr.bedgraph_analyze.store) printme() (coalispr.resources.share.ncfasta2gtf.Gtfline method) process_bamfiles() (in module coalispr.bedgraph_analyze.process_bamdata) process_graphs() (in module coalispr.bedgraph_analyze.process_bedgraphs) process_reads_for_region() (in module coalispr.bedgraph_analyze.process_bamdata) process_reference() (in module coalispr.bedgraph_analyze.process_bedgraphs) process_unselected() (in module coalispr.bedgraph_analyze.unselected) profile() (in module coalispr.resources.profilehooks) prog (in module coalispr.resources.cmd_parser) PROG_DESCRIPTION (in module coalispr.tk_gui.gui_constants) prog_frame (coalispr.tk_gui.gui_widgets.cli.Command_frames attribute) PROPR (in module coalispr.resources.constant) Python R r_tab (coalispr.tk_gui.gui_widgets.cli.Main_frame attribute) (coalispr.tk_gui.gui_widgets.menu_main.Main_frame attribute) RBP RCOL (in module coalispr.resources.constant) READCOUNTS (in module coalispr.resources.constant) READDENS (in module coalispr.resources.constant) reduce_gtf() (in module coalispr.resources.share.reduce_gtf) ref_at_clickpoint() (in module coalispr.bedgraph_analyze.genom) ref_in_segment() (in module coalispr.bedgraph_analyze.genom) REFDIR (in module coalispr.resources.constant) reference REFERENCE (in module coalispr.resources.constant) reference() (in module coalispr.bedgraph_analyze.experiment) referencetrack() (in module coalispr.bedgraph_analyze.references) REFNDIRLEVEL (in module coalispr.resources.constant) REFS (in module coalispr.resources.constant) REGCNTRS (in module coalispr.resources.constant) REGCNTS (in module coalispr.resources.constant) REGI (in module coalispr.resources.constant) region (coalispr.bedgraph_analyze.bam_counters.BamRegionCountController attribute) region() (in module coalispr.coalispr) RegionCountPanelPlotter (class in coalispr.count_analyze.panel_plotters) RegionLengthCounter (class in coalispr.bedgraph_analyze.bam_counters) REGS (in module coalispr.resources.constant) remove_odds() (in module coalispr.resources.utilities) rename_in_count_tsv() (in module coalispr.bedgraph_analyze.store) rename_in_data_tsv() (in module coalispr.bedgraph_analyze.store) rename_in_expfile() (in module coalispr.bedgraph_analyze.store) rename_unselected() (in module coalispr.bedgraph_analyze.store) repair REPAIR (in module coalispr.resources.constant) replace_dot() (in module coalispr.resources.utilities) replacelist() (in module coalispr.resources.utilities) replacelist_list() (in module coalispr.resources.utilities) report_skipped() (coalispr.bedgraph_analyze.bam_counters.BamCounterController method) (coalispr.bedgraph_analyze.bam_counters.SkipCounter method) REPS (in module coalispr.resources.constant) reset_current_combo_widget() (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame method) resizable (coalispr.tk_gui.tk_coalispr.Coalispr_app attribute) REST (in module coalispr.resources.constant) rest_commands (coalispr.tk_gui.gui_widgets.cli.Command_frames attribute) (coalispr.tk_gui.gui_widgets.menu_main.Command_frames attribute) restart() (coalispr.tk_gui.tk_coalispr.Coalispr_app method) restart_cmd (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] restart_on_submit (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] retrieve_all_chr_regions_from_tsv() (in module coalispr.bedgraph_analyze.genom) retrieve_chr_regions_from_tsv() (in module coalispr.bedgraph_analyze.genom) retrieve_merged() (in module coalispr.bedgraph_analyze.store) retrieve_merged_reference() (in module coalispr.bedgraph_analyze.references) retrieve_merged_unselected() (in module coalispr.bedgraph_analyze.store) retrieve_processed_files() (in module coalispr.bedgraph_analyze.store) revseq() (in module coalispr.resources.share.revseq) RIP RIP1 (in module coalispr.resources.constant) RIP2 (in module coalispr.resources.constant) RLENCOUNTS (in module coalispr.resources.constant) rlessx (coalispr.count_analyze.panel_plotters.LengthPanelPlotter attribute) RNA-seq RNAi rnd (coalispr.bedgraph_analyze.bam_counters.BinCounter attribute) (coalispr.bedgraph_analyze.bam_counters.LengthCounter attribute) (coalispr.bedgraph_analyze.bam_counters.RegionLengthCounter attribute) RPM rRFs rRNA run_coalispr() (in module coalispr.coalispr) S SAMBAM (in module coalispr.resources.constant) SAMPLE (in module coalispr.resources.constant) sampls (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1] savdir (coalispr.count_analyze.panel_plotters.BinPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.CountPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.LengthPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.Log2CountPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.Log2RegionCountPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1] (coalispr.count_analyze.panel_plotters.RegionCountPanelPlotter attribute) save_average_table() (in module coalispr.bedgraph_analyze.store) save_output_as() (in module coalispr.resources.plot_utilities) save_to_tsv() (coalispr.bedgraph_analyze.bam_counters.BamCounterController method) (coalispr.bedgraph_analyze.bam_counters.BamRegionCountController method) (coalispr.bedgraph_analyze.bam_counters.BinCounter method) (coalispr.bedgraph_analyze.bam_counters.Counter method) (coalispr.bedgraph_analyze.bam_counters.LengthCounter method) (coalispr.bedgraph_analyze.bam_counters.RegionLengthCounter method) (coalispr.bedgraph_analyze.bam_counters.SkipCounter method) SAVEBAM (in module coalispr.resources.constant) savedirect (coalispr.count_analyze.panel_plotters.PanelPlotter attribute) SAVEIN (in module coalispr.resources.constant) SAVEJPG (in module coalispr.resources.constant) SAVEPDF (in module coalispr.resources.constant) SAVEPNG (in module coalispr.resources.constant) SAVESVG (in module coalispr.resources.constant) SAVETSV (in module coalispr.resources.constant) SCOL (in module coalispr.resources.constant) scroll_canvas (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] scroll_height (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] scrollable_frame (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] SCROLLH (in module coalispr.tk_gui.gui_constants) SE SegmentTrack (class in coalispr.bedgraph_analyze.genom) SEGSUM (in module coalispr.resources.constant) select_from() (in module coalispr.resources.dialog) selected_item (coalispr.tk_gui.gui_widgets.cli.Cli_menu attribute) (coalispr.tk_gui.gui_widgets.menu_main.Cli_menu attribute), [1] seq_id seqend (coalispr.resources.share.ncfasta2gtf.Gtfline attribute), [1] seqid (coalispr.resources.share.ncfasta2gtf.Gtfline attribute), [1] seqstart (coalispr.resources.share.ncfasta2gtf.Gtfline attribute), [1] set_axes() (in module coalispr.resources.plot_utilities) set_bincounts() (coalispr.bedgraph_analyze.bam_counters.BamCounterController method) (coalispr.bedgraph_analyze.bam_counters.BinCounter method) (coalispr.bedgraph_analyze.bam_counters.Counter method) (coalispr.bedgraph_analyze.bam_counters.LengthCounter method) (coalispr.bedgraph_analyze.bam_counters.RegionLengthCounter method) (coalispr.bedgraph_analyze.bam_counters.SkipCounter method) set_cols() (in module coalispr.bedgraph_analyze.bam_counters) set_command_field() (coalispr.tk_gui.gui_widgets.opt.Options_frame method) set_fonts() (coalispr.tk_gui.tk_coalispr.Coalispr_app method) set_help_fields() (coalispr.tk_gui.gui_widgets.cli.Main_frame method) (coalispr.tk_gui.gui_widgets.menu_main.Main_frame method) set_loaded_command() (coalispr.tk_gui.tk_coalispr.Coalispr_app method) set_run_fields() (coalispr.tk_gui.gui_widgets.cli.Main_frame method) (coalispr.tk_gui.gui_widgets.menu_main.Main_frame method) set_style() (coalispr.tk_gui.tk_coalispr.Coalispr_app method) set_subcommand() (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame method) SETBASE (in module coalispr.resources.constant) setexp() (in module coalispr.coalispr) SGFONTSZ (in module coalispr.resources.constant) SGHEIGHT (in module coalispr.resources.constant) SGWIDTH (in module coalispr.resources.constant) SHARED (in module coalispr.resources.constant) SHIPPEDFONT (in module coalispr.tk_gui.gui_constants) SHORT (in module coalispr.resources.constant) show_chr() (in module coalispr.bedgraph_analyze.process_bedgraphs) show_mapped_vs_unmapped() (in module coalispr.bedgraph_analyze.info_plots) show_regions_vs_settings() (in module coalispr.bedgraph_analyze.info_plots) show_specific_chr() (in module coalispr.bedgraph_analyze.process_bedgraphs) show_unspecific_chr() (in module coalispr.bedgraph_analyze.process_bedgraphs) showcounts() (in module coalispr.coalispr) SHOWDISC (in module coalispr.resources.constant) showgraphs() (in module coalispr.coalispr) SHWABT (in module coalispr.tk_gui.gui_constants) siRNA size (coalispr.tk_gui.tk_coalispr.Coalispr_app attribute) sizegrip (coalispr.tk_gui.tk_coalispr.Coalispr_app attribute) sizers (coalispr.bedgraph_analyze.bam_counters.BamCounterController attribute) (coalispr.bedgraph_analyze.bam_counters.BamRegionCountController attribute) SKIP (coalispr.resources.dialog.PresentDialog attribute) (in module coalispr.resources.constant) skip_count() (coalispr.bedgraph_analyze.bam_counters.BamCounterController method) (coalispr.bedgraph_analyze.bam_counters.SkipCounter method) skip_duplicates() (coalispr.resources.share.ncfasta2gtf.Gtfline method) SkipCounter (class in coalispr.bedgraph_analyze.bam_counters) SKIPINT (in module coalispr.resources.constant) smallest2chroms() (in module coalispr.bedgraph_analyze.genom) smear SNSFNTFAM (in module coalispr.resources.constant) SNSFNTSZ (in module coalispr.resources.constant) soft-clipping sort_and_remove_duplicates() (coalispr.resources.share.ncfasta2gtf.Gtfline method) source (coalispr.resources.share.ncfasta2gtf.Gtfline attribute), [1] SOURCE (in module coalispr.resources.constant) SPAN (in module coalispr.resources.constant) specific SPECIFIC (in module coalispr.resources.constant) specific() (in module coalispr.bedgraph_analyze.compare) specified split_readlengths_index() (in module coalispr.count_analyze.load_countfile) SRCDIR (in module coalispr.resources.constant) SRCE (in module coalispr.tk_gui.gui_constants) SRCFLDR (in module coalispr.resources.constant) SRCNDIRLEVEL (in module coalispr.resources.constant) SRCPRGNAM (in module coalispr.resources.constant) start_logging() (in module coalispr.coalispr) STARV (in module coalispr.resources.constant) STEM (in module coalispr.resources.constant) stop (coalispr.resources.dialog.PresentDialog attribute) stopmsg (coalispr.resources.dialog.PresentDialog attribute) store_chromosome_data() (in module coalispr.bedgraph_analyze.store) store_chromosome_data_as_tsv() (in module coalispr.bedgraph_analyze.store) store_processed_chrindexes() (in module coalispr.bedgraph_analyze.store) storedata() (in module coalispr.coalispr) STOREPATH (in module coalispr.resources.constant) STOREPICKLE (in module coalispr.resources.constant) strand (coalispr.bedgraph_analyze.bam_counters.BamRegionCountController attribute) (coalispr.bedgraph_analyze.genom.GTFtrack attribute), [1] (coalispr.resources.share.ncfasta2gtf.Gtfline attribute), [1] STRTCMD (in module coalispr.tk_gui.gui_constants) subcom_var (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame attribute), [1] SUBCOMMAND (in module coalispr.tk_gui.gui_constants) Subcommand_frame (class in coalispr.tk_gui.gui_widgets.opt2) subcommands_info (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame attribute) subcoms (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] SUBFIGS (in module coalispr.resources.constant) submitbutton_clicked() (coalispr.tk_gui.gui_widgets.opt.Options_frame method) submittip (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] suggest_storepath() (in module coalispr.resources.dialog) svg SVG (in module coalispr.resources.constant) T TAB_LABELS (coalispr.tk_gui.gui_widgets.cli.Main_frame attribute) (coalispr.tk_gui.gui_widgets.menu_main.Main_frame attribute) TAG (in module coalispr.resources.constant) TAGBAM (in module coalispr.resources.constant) TAGCOLL (in module coalispr.resources.constant) TAGSEG (in module coalispr.resources.constant) TAGUNCOLL (in module coalispr.resources.constant) technical replicate test() (in module coalispr.coalispr) test_intervals() (in module coalispr.bedgraph_analyze.compare) textlist() (coalispr.bedgraph_analyze.genom.GTFtrack method) (coalispr.bedgraph_analyze.genom.SegmentTrack method) (coalispr.bedgraph_analyze.genom.Track method) THEME_DARK (in module coalispr.tk_gui.gui_constants) THEME_LIGHT (in module coalispr.tk_gui.gui_constants) THISALPH (in module coalispr.resources.constant) thisfile (in module coalispr.tk_gui.tk_coalispr) thisfunc() (in module coalispr.resources.utilities) timecall() (in module coalispr.resources.profilehooks) timer() (in module coalispr.resources.utilities) tip_text (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] titels (coalispr.count_analyze.panel_plotters.PanelPlotter attribute) title (coalispr.tk_gui.tk_coalispr.Coalispr_app attribute) titles (coalispr.count_analyze.panel_plotters.PanelPlotter attribute) TKFONTSIZE (in module coalispr.tk_gui.gui_constants) TKHEIGHT (in module coalispr.tk_gui.gui_constants) TKOFFSET (in module coalispr.tk_gui.gui_constants) TKRESIZABLE (in module coalispr.tk_gui.gui_constants) TKWIDTH (in module coalispr.tk_gui.gui_constants) TMP (in module coalispr.resources.constant) TOTAL (in module coalispr.resources.constant) total_raw_counts() (in module coalispr.bedgraph_analyze.process_bamdata) TOTALS (in module coalispr.resources.constant) TOTINPUT (in module coalispr.resources.constant) Track (class in coalispr.bedgraph_analyze.genom) TRACKLABEL (in module coalispr.resources.constant) tRNA TRSHLD (in module coalispr.resources.constant) try_input() (coalispr.resources.dialog.PresentDialog method) TSTREGIONS (in module coalispr.resources.constant) tsv TSV (in module coalispr.resources.constant) tsv2gtf() (in module coalispr.resources.share.gtf_frm_tsv) TSV2PKL (in module coalispr.resources.constant) tutorials (in module coalispr.resources.share.cols_from_csv_to_tab) TXTALIAS (in module coalispr.resources.constant) U UCOL (in module coalispr.resources.constant) UGAPSTST (in module coalispr.resources.constant) UInt64Index (class in coalispr.resources.numeric) unbind_mousewheel() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) uncollapsed UNCOLLAPSED (in module coalispr.resources.constant) UNIQ (in module coalispr.resources.constant) unique UNMAP (in module coalispr.resources.constant) UNMAPCOLLTP (in module coalispr.resources.constant) UNMAPPEDFIL (in module coalispr.resources.constant) UNMAPTYPE (in module coalispr.resources.constant) UNSEL (in module coalispr.resources.constant) unselected UNSELFIG (in module coalispr.resources.constant) UNSPCGAPS (in module coalispr.resources.constant) unspecific UNSPECIFIC (in module coalispr.resources.constant) unspecific() (in module coalispr.bedgraph_analyze.compare) UNSPECIFICS (in module coalispr.resources.constant) UNSPECLOG10 (in module coalispr.resources.constant) UNSPECTST (in module coalispr.resources.constant) update_args_dict() (coalispr.tk_gui.gui_widgets.opt.Options_frame method) update_multimap_count() (coalispr.bedgraph_analyze.bam_counters.BamCounterController method) (coalispr.bedgraph_analyze.bam_counters.LengthCounter method) (coalispr.bedgraph_analyze.bam_counters.RegionLengthCounter method) update_strand_count() (coalispr.bedgraph_analyze.bam_counters.BamCounterController method) (coalispr.bedgraph_analyze.bam_counters.BinCounter method) (coalispr.bedgraph_analyze.bam_counters.Counter method) (coalispr.bedgraph_analyze.bam_counters.LengthCounter method) (coalispr.bedgraph_analyze.bam_counters.RegionLengthCounter method) (coalispr.bedgraph_analyze.bam_counters.SkipCounter method) UPPR (in module coalispr.resources.constant) USAGE (coalispr.tk_gui.gui_widgets.cli.Main_frame attribute) (coalispr.tk_gui.gui_widgets.menu_main.Main_frame attribute) USEGAPS (in module coalispr.resources.constant) V VACUOL (in module coalispr.resources.constant) validate_int() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) validate_name() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) validate_namespace() (coalispr.tk_gui.gui_widgets.opt.Options_frame method) validate_region() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) var_changed() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) W WCE (in module coalispr.resources.constant) widget_group (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame attribute), [1] windows_load_font() (coalispr.tk_gui.customtkinter.font_manager.FontManager class method) WORKENV (in module coalispr.tk_gui.gui_constants) X XGRID (in module coalispr.resources.constant) xlabel (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1] XLIM0 (in module coalispr.resources.constant) XLIM00 (in module coalispr.resources.constant) XLIM1 (in module coalispr.resources.constant) XLIM11 (in module coalispr.resources.constant) XLIMMAX (in module coalispr.resources.constant) XLIMMIN (in module coalispr.resources.constant) XLIMR0 (in module coalispr.resources.constant) XLIMR1 (in module coalispr.resources.constant) XTRA (in module coalispr.resources.constant) Y yeast (in module coalispr.resources.share.cols_from_csv_to_tab) ylabel (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1] Z ZENO (in module coalispr.tk_gui.gui_constants) ZerosFrameException
