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 ACOL (in module coalispr.resources.constant) 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) 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 BASEDIR (in module coalispr.resources.constant) 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 break_xaxis() (in module coalispr.resources.plot_utilities) BREG (in module coalispr.resources.constant) BrokenLengthPanelPlotter (class in coalispr.count_analyze.panel_plotters) C 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 checkset() (in module coalispr.bedgraph_analyze.collect_bedgraphs) checkSRCDIR() (in module coalispr.bedgraph_analyze.collect_bedgraphs) chr_test() (in module coalispr.bedgraph_analyze.genom) chrnam (coalispr.bedgraph_analyze.genom.SegmentTrack attribute), [1] (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) 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.__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.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 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) COLS (in module coalispr.bedgraph_analyze.bam_counters) COMBI (in module coalispr.resources.constant) 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) 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 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 CPPHFAC (in module coalispr.resources.constant) 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_siRNA_GTF_line() (in module coalispr.resources.share.gtf_frm_tsv) CSFONTSZ (in module coalispr.resources.constant) csv 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 DATA (in module coalispr.resources.constant) DATASTOR (in module coalispr.resources.constant) DCOL (in module coalispr.resources.constant) DENSE (in module coalispr.resources.constant) depletion kits DESCRIPTION (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) 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) 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) 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] 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) 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_categories_dict() (in module coalispr.bedgraph_analyze.collect_bedgraphs) get_cols() (in module coalispr.bedgraph_analyze.bam_counters) 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_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_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_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_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_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) 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) H h99 (in module coalispr.resources.share.cols_from_csv_to_tab) 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) headers (in module coalispr.resources.share.gtf_frm_tsv) 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) 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 info() (in module coalispr.coalispr) INFOREGS (in module coalispr.resources.constant) init() (in module coalispr.coalispr) init_sns() (in module coalispr.resources.plot_utilities) INMAPCOLL (in module coalispr.resources.constant) INMAPUNCOLL (in module coalispr.resources.constant) 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) 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 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] label_frame() (in module coalispr.bedgraph_analyze.collect_bedgraphs) 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) load_bin_table_perc() (in module coalispr.count_analyze.load_countfile) load_count_table() (in module coalispr.count_analyze.load_countfile) load_file() (in module coalispr.resources.share.cols_from_csv_to_tab) 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) LOGLIM (in module coalispr.resources.constant) LOGMAX (in module coalispr.resources.constant) LOGS (in module coalispr.resources.constant) LOWLEG (in module coalispr.resources.constant) LOWR (in module coalispr.resources.constant) LPPHFAC (in module coalispr.resources.constant) M 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) make_constant() (in module coalispr.resources.constant_in.make_constant) make_parser() (in module coalispr.resources.cmd_parser) 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) 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.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 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) 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 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) P2TDELIM (in module coalispr.resources.constant) PALETTE (in module coalispr.resources.constant) PanelPlotter (class in coalispr.count_analyze.panel_plotters) pattern (coalispr.resources.dialog.PresentDialog attribute), [1] 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) PROPR (in module coalispr.resources.constant) Python R 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) REST (in module coalispr.resources.constant) 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 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) SE SegmentTrack (class in coalispr.bedgraph_analyze.genom) SEGSUM (in module coalispr.resources.constant) select_from() (in module coalispr.resources.dialog) 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) 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) 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) siRNA 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) SRCFLDR (in module coalispr.resources.constant) SRCNDIRLEVEL (in module coalispr.resources.constant) SRCPRGNAM (in module coalispr.resources.constant) 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] SUBFIGS (in module coalispr.resources.constant) suggest_storepath() (in module coalispr.resources.dialog) svg SVG (in module coalispr.resources.constant) T 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) THISALPH (in module coalispr.resources.constant) thisfunc() (in module coalispr.resources.utilities) timer() (in module coalispr.resources.utilities) titels (coalispr.count_analyze.panel_plotters.PanelPlotter attribute) titles (coalispr.count_analyze.panel_plotters.PanelPlotter attribute) 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) 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_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) USEGAPS (in module coalispr.resources.constant) V VACUOL (in module coalispr.resources.constant) W WCE (in module coalispr.resources.constant) 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 ZerosFrameException
