Index

A

add_colorbar_args() (rnavigate.plots.Plot method) (rnavigate.plots.plots.Plot method) add_lines() (rnavigate.plots.Mol method) (rnavigate.plots.mol.Mol method) add_metric_defaults() (rnavigate.data.Data method) (rnavigate.data.data.Data method) add_pairs() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) adjust_spines() (in module rnavigate.plots) (in module rnavigate.plots.functions) (in module rnavigate.plots.functions.functions) Alignment (class in rnavigate.plots) (class in rnavigate.plots.alignment)

AlignmentChain (class in rnavigate.data) (class in rnavigate.data.alignments) AllPossible (class in rnavigate.data) (class in rnavigate.data.interactions) Annotation (class in rnavigate.data) (class in rnavigate.data.annotation) AP (class in rnavigate.plots) (class in rnavigate.plots.arc) as_interactions() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) average_columns() (rnavigate.analysis.fragmapper.FragmapperReplicates method) (rnavigate.analysis.FragmapperReplicates method)

B

BaseAlignment (class in rnavigate.data.alignments) BedFile (class in rnavigate.transcriptomics) (class in rnavigate.transcriptomics.bed) boolean (rnavigate.data.Annotation property) (rnavigate.data.annotation.Annotation property) (rnavigate.data.secondary_structure.SecondaryStructure property) (rnavigate.data.SecondaryStructure property) box_xtick_labels() (in module rnavigate.plots) (in module rnavigate.plots.functions) (in module rnavigate.plots.functions.functions)

break_noncanonical_pairs() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) break_pairs_nts() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) break_pairs_region() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) break_singleton_pairs() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method)

C

calc_profile() (rnavigate.analysis.logcompare.LogProfile method) calculate_deltashape() (rnavigate.analysis.DeltaSHAPE method) (rnavigate.analysis.deltashape.DeltaSHAPE method) (rnavigate.analysis.deltashape.DeltaSHAPEProfile method) (rnavigate.analysis.DeltaSHAPEProfile method) calculate_gini_index() (rnavigate.data.Profile method) (rnavigate.data.profile.Profile method) calculate_windows() (rnavigate.data.Profile method) (rnavigate.data.profile.Profile method) center() (rnavigate.data.secondary_structure.StructureCoordinates method) (rnavigate.data.StructureCoordinates method) Circle (class in rnavigate.plots) (class in rnavigate.plots.circle) clip_spines() (in module rnavigate.plots) (in module rnavigate.plots.functions) (in module rnavigate.plots.functions.functions) cmap (rnavigate.data.Data property) (rnavigate.data.data.Data property) color_column (rnavigate.data.Data property) (rnavigate.data.data.Data property)

ColorBar (class in rnavigate.plots) (class in rnavigate.plots.plots) colors (rnavigate.data.Data property) (rnavigate.data.data.Data property) compute_ppv_sens() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) contact distance contact_distance() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) convert_sequence() (in module rnavigate.data.alignments) copy() (rnavigate.data.Interactions method) (rnavigate.data.interactions.Interactions method) (rnavigate.data.Profile method) (rnavigate.data.profile.Profile method) (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) count_filter() (rnavigate.data.Interactions method) (rnavigate.data.interactions.Interactions method) create_eclip_table() (in module rnavigate.transcriptomics) (in module rnavigate.transcriptomics.eclip)

D

DanceMaP (class in rnavigate.data) (class in rnavigate.data.profile) Data (class in rnavigate.data) (class in rnavigate.data.data) Data keyword Data object data_specific_filter() (rnavigate.data.Interactions method) (rnavigate.data.interactions.Interactions method) (rnavigate.data.interactions.PairingProbability method) (rnavigate.data.interactions.PAIRMaP method) (rnavigate.data.interactions.RINGMaP method) (rnavigate.data.PairingProbability method) (rnavigate.data.PAIRMaP method) (rnavigate.data.RINGMaP method)

DeltaProfile (class in rnavigate.data) (class in rnavigate.data.profile) DeltaSHAPE (class in rnavigate.analysis) (class in rnavigate.analysis.deltashape) DeltaSHAPEProfile (class in rnavigate.analysis) (class in rnavigate.analysis.deltashape) DistHist (class in rnavigate.plots) (class in rnavigate.plots.disthist) domains() (in module rnavigate.data) (in module rnavigate.data.annotation) download_eclip_peaks() (in module rnavigate.transcriptomics) (in module rnavigate.transcriptomics.eclip)

E

eCLIPDatabase (class in rnavigate.transcriptomics) (class in rnavigate.transcriptomics.eclip)

error_column (rnavigate.data.Data property) (rnavigate.data.data.Data property)

F

fill_mismatches() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) filter() (rnavigate.data.Interactions method) (rnavigate.data.interactions.Interactions method) filter_interactions() (rnavigate.Sample method), [1] finalize() (rnavigate.plots.LinReg method) (rnavigate.plots.linreg.LinReg method) flip() (rnavigate.data.secondary_structure.StructureCoordinates method) (rnavigate.data.StructureCoordinates method) FragMaP (class in rnavigate.analysis) (class in rnavigate.analysis.fragmapper) Fragmapper (class in rnavigate.analysis) (class in rnavigate.analysis.fragmapper) FragmapperReplicates (class in rnavigate.analysis) (class in rnavigate.analysis.fragmapper)

from_array() (rnavigate.data.Profile class method) (rnavigate.data.profile.Profile class method) from_boolean_array() (rnavigate.data.Annotation class method) (rnavigate.data.annotation.Annotation class method) from_pairs_list() (rnavigate.data.secondary_structure.SecondaryStructure class method) (rnavigate.data.SecondaryStructure class method) from_rnaframework() (rnavigate.data.profile.SHAPEMaP class method) (rnavigate.data.SHAPEMaP class method) from_sequence() (rnavigate.data.secondary_structure.SecondaryStructure class method) (rnavigate.data.SecondaryStructure class method) from_sites() (rnavigate.data.Annotation method) (rnavigate.data.annotation.Annotation method) from_spans() (rnavigate.data.Annotation method) (rnavigate.data.annotation.Annotation method)

G

get_aligned_data() (rnavigate.data.Annotation method) (rnavigate.data.annotation.Annotation method) (rnavigate.data.annotation.Motif method) (rnavigate.data.annotation.ORFs method) (rnavigate.data.data.Sequence method) (rnavigate.data.Interactions method) (rnavigate.data.interactions.Interactions method) (rnavigate.data.Motif method) (rnavigate.data.ORFs method) (rnavigate.data.Profile method) (rnavigate.data.profile.Profile method) (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) (rnavigate.data.Sequence method) get_alignment() (rnavigate.data.alignments.SequenceAlignment method) (rnavigate.data.alignments.StructureAlignment method) (rnavigate.data.SequenceAlignment method) (rnavigate.data.StructureAlignment method) get_annotation() (rnavigate.analysis.FragMaP method) (rnavigate.analysis.fragmapper.FragMaP method) (rnavigate.transcriptomics.bed.BedFile method) (rnavigate.transcriptomics.BedFile method) (rnavigate.transcriptomics.eclip.eCLIPDatabase method) (rnavigate.transcriptomics.eCLIPDatabase method) get_annotations() (rnavigate.transcriptomics.bed.BedFile method) (rnavigate.transcriptomics.BedFile method) get_ax() (rnavigate.plots.Plot method) (rnavigate.plots.plots.Plot method) (rnavigate.plots.Skyline method) (rnavigate.plots.skyline.Skyline method) get_cds_annotation() (rnavigate.transcriptomics.Transcript method) (rnavigate.transcriptomics.transcriptome.Transcript method) get_cds_domains() (rnavigate.transcriptomics.Transcript method) (rnavigate.transcriptomics.transcriptome.Transcript method) get_cell_target_data() (rnavigate.transcriptomics.eclip.eCLIPDatabase method) (rnavigate.transcriptomics.eCLIPDatabase method) get_center_point() (rnavigate.data.secondary_structure.StructureCoordinates method) (rnavigate.data.StructureCoordinates method) get_cmap() (rnavigate.data.colors.ScalarMappable method) (rnavigate.data.ScalarMappable method) get_colors() (rnavigate.data.data.Sequence method) (rnavigate.data.Sequence method) get_colors_from_annotations() (rnavigate.data.data.Sequence method) (rnavigate.data.Sequence method) get_colors_from_positions() (rnavigate.data.data.Sequence method) (rnavigate.data.Sequence method) get_colors_from_profile() (rnavigate.data.data.Sequence method) (rnavigate.data.Sequence method) get_colors_from_sequence() (rnavigate.data.data.Sequence method) (rnavigate.data.Sequence method) get_colors_from_structure() (rnavigate.data.data.Sequence method) (rnavigate.data.Sequence method) get_contrasting_colors() (in module rnavigate.plots) (in module rnavigate.plots.functions) (in module rnavigate.plots.functions.functions) get_coordinate_df() (rnavigate.transcriptomics.Transcript method) (rnavigate.transcriptomics.transcriptome.Transcript method) get_data() (rnavigate.Sample method), [1] get_dataframe() (rnavigate.analysis.FragMaP method) (rnavigate.analysis.fragmapper.FragMaP method) get_density_profile() (rnavigate.transcriptomics.bed.BedFile method) (rnavigate.transcriptomics.BedFile method) get_distance() (rnavigate.data.PDB method) (rnavigate.data.pdb.PDB method) get_distance_matrix() (rnavigate.data.PDB method) (rnavigate.data.pdb.PDB method) (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) get_dotbracket() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) get_eclip_data() (rnavigate.transcriptomics.eclip.eCLIPDatabase method) (rnavigate.transcriptomics.eCLIPDatabase method) get_eclip_density() (rnavigate.transcriptomics.eclip.eCLIPDatabase method) (rnavigate.transcriptomics.eCLIPDatabase method) get_enhancements_annotation() (rnavigate.analysis.deltashape.DeltaSHAPEProfile method) (rnavigate.analysis.DeltaSHAPEProfile method) get_entropy_profile() (rnavigate.data.interactions.PairingProbability method) (rnavigate.data.PairingProbability method) get_exon_annotation() (rnavigate.transcriptomics.Transcript method) (rnavigate.transcriptomics.transcriptome.Transcript method) get_exon_domains() (rnavigate.transcriptomics.Transcript method) (rnavigate.transcriptomics.transcriptome.Transcript method) get_helices() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) get_human_dotbracket() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) get_ij_colors() (rnavigate.data.Interactions method) (rnavigate.data.interactions.Interactions method) get_interactions_df() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) get_inverse_alignment() (rnavigate.data.AlignmentChain method) (rnavigate.data.alignments.AlignmentChain method) (rnavigate.data.alignments.BaseAlignment method) (rnavigate.data.alignments.SequenceAlignment method) (rnavigate.data.alignments.StructureAlignment method) (rnavigate.data.SequenceAlignment method) (rnavigate.data.StructureAlignment method) get_junction_nts() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method)

get_junctions_annotation() (rnavigate.transcriptomics.Transcript method) (rnavigate.transcriptomics.transcriptome.Transcript method) get_keywords() (rnavigate.analysis.check_sequence.SequenceChecker method) (rnavigate.analysis.SequenceChecker method) get_mapping() (rnavigate.data.AlignmentChain method) (rnavigate.data.alignments.AlignmentChain method) (rnavigate.data.alignments.BaseAlignment method) (rnavigate.data.alignments.SequenceAlignment method) (rnavigate.data.alignments.StructureAlignment method) (rnavigate.data.SequenceAlignment method) (rnavigate.data.StructureAlignment method) get_nonredundant_ct() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) get_norm() (rnavigate.data.colors.ScalarMappable method) (rnavigate.data.ScalarMappable method) get_nt_ticks() (in module rnavigate.plots) (in module rnavigate.plots.functions) (in module rnavigate.plots.functions.functions) get_orientation() (rnavigate.plots.Mol method) (rnavigate.plots.mol.Mol method) get_paired_nts() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) get_pairs() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) get_pdb_idx() (rnavigate.data.PDB method) (rnavigate.data.pdb.PDB method) get_plotting_dataframe() (rnavigate.data.Profile method) (rnavigate.data.profile.Profile method) get_profile() (rnavigate.transcriptomics.bed.BedFile method) (rnavigate.transcriptomics.BedFile method) (rnavigate.transcriptomics.eclip.eCLIPDatabase method) (rnavigate.transcriptomics.eCLIPDatabase method) get_protections_annotation() (rnavigate.analysis.deltashape.DeltaSHAPEProfile method) (rnavigate.analysis.DeltaSHAPEProfile method) get_pseudoknots() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) get_region() (rnavigate.data.data.Sequence method) (rnavigate.data.Sequence method) get_region_data() (rnavigate.data.data.Sequence method) (rnavigate.data.Sequence method) get_rows_columns() (rnavigate.plots.Plot method) (rnavigate.plots.plots.Plot method) (rnavigate.plots.Profile method) (rnavigate.plots.profile.Profile method) (rnavigate.plots.QC method) (rnavigate.plots.qc.QC method) (rnavigate.plots.ROC method) (rnavigate.plots.roc.ROC method) (rnavigate.plots.Skyline method) (rnavigate.plots.skyline.Skyline method) get_seq_from_dataframe() (rnavigate.data.data.Sequence method) (rnavigate.data.Sequence method) get_seq_idx() (rnavigate.data.PDB method) (rnavigate.data.pdb.PDB method) get_sequence() (rnavigate.data.PDB method) (rnavigate.data.pdb.PDB method) (rnavigate.transcriptomics.Transcriptome method) (rnavigate.transcriptomics.transcriptome.Transcriptome method) get_sequence_from_seqres() (rnavigate.data.PDB method) (rnavigate.data.pdb.PDB method) get_sequences() (rnavigate.analysis.check_sequence.SequenceChecker method) (rnavigate.analysis.SequenceChecker method) (rnavigate.transcriptomics.Transcriptome method) (rnavigate.transcriptomics.transcriptome.Transcriptome method) get_sites() (rnavigate.data.Annotation method) (rnavigate.data.annotation.Annotation method) get_sorted_data() (rnavigate.data.Interactions method) (rnavigate.data.interactions.Interactions method) (rnavigate.data.interactions.PAIRMaP method) (rnavigate.data.interactions.RINGMaP method) (rnavigate.data.PAIRMaP method) (rnavigate.data.RINGMaP method) get_spans_from_motif() (rnavigate.data.annotation.Motif method) (rnavigate.data.Motif method) get_spans_from_orf() (rnavigate.data.annotation.ORFs method) (rnavigate.data.ORFs method) get_structure_elements() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) get_subsequences() (rnavigate.data.Annotation method) (rnavigate.data.annotation.Annotation method) get_target_sequence() (rnavigate.data.alignments.BaseAlignment method) get_transcript() (rnavigate.transcriptomics.Transcriptome method) (rnavigate.transcriptomics.transcriptome.Transcriptome method) get_transcripts() (rnavigate.transcriptomics.Transcriptome method) (rnavigate.transcriptomics.transcriptome.Transcriptome method) get_tx_coordinate() (rnavigate.transcriptomics.Transcript method) (rnavigate.transcriptomics.transcriptome.Transcript method) get_tx_range() (rnavigate.transcriptomics.Transcript method) (rnavigate.transcriptomics.transcriptome.Transcript method) get_unpaired_nts() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) get_viewer() (rnavigate.plots.Mol method) (rnavigate.plots.mol.Mol method) get_which_sequences() (rnavigate.analysis.check_sequence.SequenceChecker method) (rnavigate.analysis.SequenceChecker method) get_xyz_coord() (rnavigate.data.PDB method) (rnavigate.data.pdb.PDB method)

H

Heatmap (class in rnavigate.plots) (class in rnavigate.plots.heatmap)

hide_cylinders() (rnavigate.plots.Mol method) (rnavigate.plots.mol.Mol method)

I

idx index indices inherit_data() (rnavigate.Sample method), [1] interactions Interactions (class in rnavigate.data) (class in rnavigate.data.interactions)

interactions2 is_equivalent_to() (rnavigate.data.colors.ScalarMappable method) (rnavigate.data.ScalarMappable method) is_valid_idx() (rnavigate.data.PDB method) (rnavigate.data.pdb.PDB method)

L

length (rnavigate.data.data.Sequence property) (rnavigate.data.Sequence property) LinReg (class in rnavigate.plots) (class in rnavigate.plots.linreg) load_replicates() (rnavigate.analysis.logcompare.LogProfile method) LogCompare (class in rnavigate.analysis) (class in rnavigate.analysis.logcompare)

LogProfile (class in rnavigate.analysis.logcompare) lookup_alignment() (in module rnavigate.data) (in module rnavigate.data.alignments) LowSS (class in rnavigate.analysis) (class in rnavigate.analysis.lowss)

M

make_boxplot() (rnavigate.plots.QC method) (rnavigate.plots.qc.QC method) map_dataframe() (rnavigate.data.alignments.BaseAlignment method) map_indices() (rnavigate.data.alignments.BaseAlignment method) map_nucleotide_dataframe() (rnavigate.data.alignments.BaseAlignment method) map_positions() (rnavigate.data.alignments.BaseAlignment method) map_values() (rnavigate.data.alignments.BaseAlignment method) mask_on_distance() (rnavigate.data.Interactions method) (rnavigate.data.interactions.Interactions method) mask_on_position() (rnavigate.data.Interactions method) (rnavigate.data.interactions.Interactions method) mask_on_profile() (rnavigate.data.Interactions method) (rnavigate.data.interactions.Interactions method) mask_on_sequence() (rnavigate.data.Interactions method) (rnavigate.data.interactions.Interactions method) mask_on_structure() (rnavigate.data.Interactions method) (rnavigate.data.interactions.Interactions method) mask_on_values() (rnavigate.data.Interactions method) (rnavigate.data.interactions.Interactions method) merge_samples() (rnavigate.analysis.fragmapper.FragmapperReplicates method) (rnavigate.analysis.FragmapperReplicates method) metric (rnavigate.data.Data property) (rnavigate.data.data.Data property) metric_abbreviate() (rnavigate.plots.SM method) (rnavigate.plots.sm.SM method) module rnavigate, [1] rnavigate.analysis rnavigate.analysis.auroc rnavigate.analysis.check_sequence rnavigate.analysis.deltashape rnavigate.analysis.fragmapper rnavigate.analysis.logcompare rnavigate.analysis.lowss rnavigate.data rnavigate.data.alignments rnavigate.data.annotation rnavigate.data.colors rnavigate.data.data rnavigate.data.interactions rnavigate.data.pdb rnavigate.data.profile rnavigate.data.secondary_structure rnavigate.data_loading rnavigate.examples rnavigate.examples.rmrp_data rnavigate.examples.rnasep_data rnavigate.examples.rrna_fragmap_data rnavigate.examples.tpp_data rnavigate.helper_functions rnavigate.plots rnavigate.plots.alignment rnavigate.plots.arc rnavigate.plots.circle rnavigate.plots.disthist rnavigate.plots.functions rnavigate.plots.functions.circle rnavigate.plots.functions.functions rnavigate.plots.functions.ss rnavigate.plots.functions.tracks rnavigate.plots.heatmap rnavigate.plots.linreg rnavigate.plots.mol rnavigate.plots.ntdist rnavigate.plots.plots rnavigate.plots.profile rnavigate.plots.qc rnavigate.plots.roc rnavigate.plots.skyline rnavigate.plots.sm rnavigate.plots.ss rnavigate.plotting_functions rnavigate.rnavigate rnavigate.styles rnavigate.transcriptomics rnavigate.transcriptomics.bed rnavigate.transcriptomics.eclip rnavigate.transcriptomics.transcriptome

Mol (class in rnavigate.plots) (class in rnavigate.plots.mol) Motif (class in rnavigate.data) (class in rnavigate.data.annotation)

N

NarrowPeak (class in rnavigate.transcriptomics) (class in rnavigate.transcriptomics.bed) norm_boxplot() (rnavigate.data.Profile method) (rnavigate.data.profile.Profile method) norm_eDMS() (rnavigate.data.Profile method) (rnavigate.data.profile.Profile method) norm_percentiles() (rnavigate.data.Profile method) (rnavigate.data.profile.Profile method) normalize() (rnavigate.data.Profile method) (rnavigate.data.profile.Profile method) normalize_dtypes() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) normalize_external() (rnavigate.data.Profile method) (rnavigate.data.profile.Profile method)

normalize_sequence() (in module rnavigate.data) (in module rnavigate.data.data) (rnavigate.data.data.Sequence method) (rnavigate.data.Profile method) (rnavigate.data.profile.Profile method) (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) (rnavigate.data.Sequence method) nts (rnavigate.data.secondary_structure.SecondaryStructure property) (rnavigate.data.SecondaryStructure property) NucleotideDistribution (class in rnavigate.plots) (class in rnavigate.plots.ntdist)

O

ORFs (class in rnavigate.data) (class in rnavigate.data.annotation)

P

pair_nts (rnavigate.data.secondary_structure.SecondaryStructure property) (rnavigate.data.SecondaryStructure property) PairingProbability (class in rnavigate.data) (class in rnavigate.data.interactions) PAIRMaP (class in rnavigate.data) (class in rnavigate.data.interactions) PDB (class in rnavigate.data) (class in rnavigate.data.pdb) Plot (class in rnavigate.plots) (class in rnavigate.plots.plots) plot() (rnavigate.analysis.DeltaSHAPE method) (rnavigate.analysis.deltashape.DeltaSHAPE method) plot_alignment() (in module rnavigate), [1] plot_annotation_circle() (in module rnavigate.plots) (in module rnavigate.plots.functions) (in module rnavigate.plots.functions.circle) plot_annotation_ss() (in module rnavigate.plots) (in module rnavigate.plots.functions) (in module rnavigate.plots.functions.ss) plot_annotation_track() (in module rnavigate.plots) (in module rnavigate.plots.functions) (in module rnavigate.plots.functions.tracks) plot_arcs() (in module rnavigate), [1] plot_arcs_compare() (in module rnavigate), [1] plot_auroc() (rnavigate.analysis.auroc.WindowedAUROC method) (rnavigate.analysis.WindowedAUROC method) plot_basepairs_ss() (in module rnavigate.plots) (in module rnavigate.plots.functions) (in module rnavigate.plots.functions.ss) plot_circle() (in module rnavigate), [1] plot_colorbars() (rnavigate.plots.Plot method) (rnavigate.plots.plots.Plot method) plot_contour_distances() (rnavigate.plots.Heatmap method) (rnavigate.plots.heatmap.Heatmap method) plot_contour_regions() (rnavigate.plots.Heatmap method) (rnavigate.plots.heatmap.Heatmap method) plot_data() (rnavigate.plots.Alignment method) (rnavigate.plots.alignment.Alignment method) (rnavigate.plots.AP method) (rnavigate.plots.arc.AP method) (rnavigate.plots.Circle method) (rnavigate.plots.circle.Circle method) (rnavigate.plots.ColorBar method) (rnavigate.plots.DistHist method) (rnavigate.plots.disthist.DistHist method) (rnavigate.plots.Heatmap method) (rnavigate.plots.heatmap.Heatmap method) (rnavigate.plots.LinReg method) (rnavigate.plots.linreg.LinReg method) (rnavigate.plots.Mol method) (rnavigate.plots.mol.Mol method) (rnavigate.plots.ntdist.NucleotideDistribution method) (rnavigate.plots.NucleotideDistribution method) (rnavigate.plots.Plot method) (rnavigate.plots.plots.ColorBar method) (rnavigate.plots.plots.Plot method) (rnavigate.plots.Profile method) (rnavigate.plots.profile.Profile method) (rnavigate.plots.QC method) (rnavigate.plots.qc.QC method) (rnavigate.plots.ROC method) (rnavigate.plots.roc.ROC method) (rnavigate.plots.Skyline method) (rnavigate.plots.skyline.Skyline method) (rnavigate.plots.SM method) (rnavigate.plots.sm.SM method) (rnavigate.plots.SS method) (rnavigate.plots.ss.SS method) plot_disthist() (in module rnavigate), [1] plot_domain_track() (in module rnavigate.plots) (in module rnavigate.plots.functions) (in module rnavigate.plots.functions.tracks) plot_experimental_distances() (rnavigate.plots.DistHist method) (rnavigate.plots.disthist.DistHist method) plot_heatmap() (in module rnavigate), [1] plot_heatmap_data() (rnavigate.plots.Heatmap method) (rnavigate.plots.heatmap.Heatmap method) plot_interactions() (rnavigate.plots.Mol method) (rnavigate.plots.mol.Mol method) plot_interactions_arcs() (in module rnavigate.plots) (in module rnavigate.plots.functions) (in module rnavigate.plots.functions.functions) plot_interactions_circle() (in module rnavigate.plots) (in module rnavigate.plots.functions) (in module rnavigate.plots.functions.circle) plot_interactions_ss() (in module rnavigate.plots) (in module rnavigate.plots.functions) (in module rnavigate.plots.functions.ss)

plot_kde_data() (rnavigate.plots.Heatmap method) (rnavigate.plots.heatmap.Heatmap method) plot_linreg() (in module rnavigate), [1] plot_lowss() (rnavigate.analysis.LowSS method) (rnavigate.analysis.lowss.LowSS method) plot_mol() (in module rnavigate), [1] plot_mutations_per_molecule() (rnavigate.plots.QC method) (rnavigate.plots.qc.QC method) plot_ntdist() (in module rnavigate), [1] plot_nucleotides_ss() (in module rnavigate.plots) (in module rnavigate.plots.functions) (in module rnavigate.plots.functions.ss) plot_options() (in module rnavigate), [1] plot_positions_ss() (in module rnavigate.plots) (in module rnavigate.plots.functions) (in module rnavigate.plots.functions.ss) plot_profile() (in module rnavigate), [1] plot_profile_bars() (in module rnavigate.plots) (in module rnavigate.plots.functions) (in module rnavigate.plots.functions.functions) plot_profile_skyline() (in module rnavigate.plots) (in module rnavigate.plots.functions) (in module rnavigate.plots.functions.functions) plot_qc() (in module rnavigate), [1] plot_read_lengths() (rnavigate.plots.QC method) (rnavigate.plots.qc.QC method) plot_regression() (rnavigate.plots.LinReg method) (rnavigate.plots.linreg.LinReg method) plot_roc() (in module rnavigate), [1] plot_scatter() (rnavigate.analysis.Fragmapper method) (rnavigate.analysis.fragmapper.Fragmapper method) (rnavigate.analysis.fragmapper.FragmapperReplicates method) (rnavigate.analysis.FragmapperReplicates method) plot_sequence_alignment() (in module rnavigate.plots) (in module rnavigate.plots.functions) (in module rnavigate.plots.functions.functions) plot_sequence_ss() (in module rnavigate.plots) (in module rnavigate.plots.functions) (in module rnavigate.plots.functions.ss) plot_sequence_track() (in module rnavigate.plots) (in module rnavigate.plots.functions) (in module rnavigate.plots.functions.tracks) plot_shapemapper() (in module rnavigate), [1] plot_skyline() (in module rnavigate), [1] plot_sm_depth() (rnavigate.plots.SM method) (rnavigate.plots.sm.SM method) plot_sm_profile() (rnavigate.plots.SM method) (rnavigate.plots.sm.SM method) plot_sm_rates() (rnavigate.plots.SM method) (rnavigate.plots.sm.SM method) plot_ss() (in module rnavigate), [1] plot_structure_distances() (rnavigate.plots.DistHist method) (rnavigate.plots.disthist.DistHist method) plot_structure_ss() (in module rnavigate.plots) (in module rnavigate.plots.functions) (in module rnavigate.plots.functions.ss) pos position positions print() (rnavigate.data.alignments.SequenceAlignment method) (rnavigate.data.SequenceAlignment method) print_alignments() (rnavigate.analysis.check_sequence.SequenceChecker method) (rnavigate.analysis.SequenceChecker method) print_all_changes() (rnavigate.data.alignments.SequenceAlignment method) (rnavigate.data.SequenceAlignment method) print_all_peaks() (rnavigate.transcriptomics.eclip.eCLIPDatabase method) (rnavigate.transcriptomics.eCLIPDatabase method) print_cigar() (rnavigate.data.alignments.SequenceAlignment method) (rnavigate.data.SequenceAlignment method) print_data_keywords() (rnavigate.Sample method), [1] print_mulitple_sequence_alignment() (rnavigate.analysis.check_sequence.SequenceChecker method) (rnavigate.analysis.SequenceChecker method) print_new_file() (rnavigate.data.Interactions method) (rnavigate.data.interactions.Interactions method) print_number_of_changes() (rnavigate.data.alignments.SequenceAlignment method) (rnavigate.data.SequenceAlignment method) print_peaks() (rnavigate.transcriptomics.eclip.eCLIPDatabase method) (rnavigate.transcriptomics.eCLIPDatabase method) print_which_sequences() (rnavigate.analysis.check_sequence.SequenceChecker method) (rnavigate.analysis.SequenceChecker method) profile Profile (class in rnavigate.data) (class in rnavigate.data.profile) (class in rnavigate.plots) (class in rnavigate.plots.profile)

Q

QC (class in rnavigate.plots) (class in rnavigate.plots.qc)

R

read_bps() (rnavigate.data.interactions.PairingProbability method) (rnavigate.data.PairingProbability method) read_ct() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) read_cte() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) read_dotbracket() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) read_fasta() (rnavigate.data.data.Sequence method) (rnavigate.data.Sequence method) read_file() (rnavigate.data.DanceMaP method) (rnavigate.data.Data method) (rnavigate.data.data.Data method) (rnavigate.data.interactions.PAIRMaP method) (rnavigate.data.interactions.RINGMaP method) (rnavigate.data.interactions.SHAPEJuMP method) (rnavigate.data.PAIRMaP method) (rnavigate.data.profile.DanceMaP method) (rnavigate.data.RINGMaP method) (rnavigate.data.SHAPEJuMP method) read_forna() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) read_log() (rnavigate.data.profile.SHAPEMaP method) (rnavigate.data.SHAPEMaP method) read_nsd() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) read_pdb() (rnavigate.data.PDB method) (rnavigate.data.pdb.PDB method) read_r2dt() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) read_txt() (rnavigate.data.interactions.PairingProbability method) (rnavigate.data.PairingProbability method) read_varna() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) read_xrna() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) recreation_kwargs (rnavigate.analysis.FragMaP property) (rnavigate.analysis.fragmapper.FragMaP property) (rnavigate.data.DanceMaP property) (rnavigate.data.Profile property) (rnavigate.data.profile.DanceMaP property) (rnavigate.data.profile.Profile property) rescale() (rnavigate.analysis.logcompare.LogProfile method) reset() (rnavigate.analysis.check_sequence.SequenceChecker method) (rnavigate.analysis.SequenceChecker method) reset_lowss() (rnavigate.analysis.LowSS method) (rnavigate.analysis.lowss.LowSS method) reset_mask() (rnavigate.data.Interactions method) (rnavigate.data.interactions.Interactions method) reset_window() (rnavigate.analysis.LowSS method) (rnavigate.analysis.lowss.LowSS method) resolve_conflicts() (rnavigate.data.Interactions method) (rnavigate.data.interactions.Interactions method) RINGMaP (class in rnavigate.data) (class in rnavigate.data.interactions) rnavigate module, [1] rnavigate.analysis module rnavigate.analysis.auroc module rnavigate.analysis.check_sequence module rnavigate.analysis.deltashape module rnavigate.analysis.fragmapper module rnavigate.analysis.logcompare module rnavigate.analysis.lowss module rnavigate.data module rnavigate.data.alignments module rnavigate.data.annotation module rnavigate.data.colors module rnavigate.data.data module rnavigate.data.interactions module

rnavigate.data.pdb module rnavigate.data.profile module rnavigate.data.secondary_structure module rnavigate.data_loading module rnavigate.examples module rnavigate.examples.rmrp_data module rnavigate.examples.rnasep_data module rnavigate.examples.rrna_fragmap_data module rnavigate.examples.tpp_data module rnavigate.helper_functions module rnavigate.plots module rnavigate.plots.alignment module rnavigate.plots.arc module rnavigate.plots.circle module rnavigate.plots.disthist module rnavigate.plots.functions module rnavigate.plots.functions.circle module rnavigate.plots.functions.functions module rnavigate.plots.functions.ss module rnavigate.plots.functions.tracks module rnavigate.plots.heatmap module rnavigate.plots.linreg module rnavigate.plots.mol module rnavigate.plots.ntdist module rnavigate.plots.plots module rnavigate.plots.profile module rnavigate.plots.qc module rnavigate.plots.roc module rnavigate.plots.skyline module rnavigate.plots.sm module rnavigate.plots.ss module rnavigate.plotting_functions module rnavigate.rnavigate module rnavigate.styles module rnavigate.transcriptomics module rnavigate.transcriptomics.bed module rnavigate.transcriptomics.eclip module rnavigate.transcriptomics.transcriptome module RNPMaP (class in rnavigate.data) (class in rnavigate.data.profile) ROC (class in rnavigate.plots) (class in rnavigate.plots.roc) rotate() (rnavigate.data.secondary_structure.StructureCoordinates method) (rnavigate.data.StructureCoordinates method)

S

Sample (class in rnavigate), [1] save() (rnavigate.plots.Mol method) (rnavigate.plots.mol.Mol method) (rnavigate.plots.Plot method) (rnavigate.plots.plots.Plot method) ScalarMappable (class in rnavigate.data) (class in rnavigate.data.colors) scale() (rnavigate.data.secondary_structure.StructureCoordinates method) (rnavigate.data.StructureCoordinates method) SecondaryStructure (class in rnavigate.data) (class in rnavigate.data.secondary_structure) sequence Sequence (class in rnavigate.data) (class in rnavigate.data.data) SequenceAlignment (class in rnavigate.data) (class in rnavigate.data.alignments) SequenceChecker (class in rnavigate.analysis) (class in rnavigate.analysis.check_sequence) SequenceCircle (class in rnavigate.data) (class in rnavigate.data.secondary_structure) set_3d_distances() (rnavigate.data.Interactions method) (rnavigate.data.interactions.Interactions method) set_alignment() (in module rnavigate.data) (in module rnavigate.data.alignments) set_as_default() (rnavigate.Sample method), [1] set_as_default_alignment() (rnavigate.data.alignments.StructureAlignment method) (rnavigate.data.StructureAlignment method) set_axis() (rnavigate.plots.AP method) (rnavigate.plots.arc.AP method) (rnavigate.plots.Circle method) (rnavigate.plots.circle.Circle method) (rnavigate.plots.Profile method) (rnavigate.plots.profile.Profile method) (rnavigate.plots.Skyline method) (rnavigate.plots.skyline.Skyline method) set_colors() (rnavigate.plots.Mol method) (rnavigate.plots.mol.Mol method) set_data() (rnavigate.Sample method), [1] set_distances() (rnavigate.data.Interactions method) (rnavigate.data.interactions.Interactions method) set_figure_size() (rnavigate.plots.Alignment method) (rnavigate.plots.alignment.Alignment method) (rnavigate.plots.AP method) (rnavigate.plots.arc.AP method) (rnavigate.plots.Circle method) (rnavigate.plots.circle.Circle method) (rnavigate.plots.ColorBar method) (rnavigate.plots.DistHist method) (rnavigate.plots.disthist.DistHist method) (rnavigate.plots.Heatmap method) (rnavigate.plots.heatmap.Heatmap method) (rnavigate.plots.LinReg method) (rnavigate.plots.linreg.LinReg method) (rnavigate.plots.ntdist.NucleotideDistribution method) (rnavigate.plots.NucleotideDistribution method) (rnavigate.plots.Plot method) (rnavigate.plots.plots.ColorBar method) (rnavigate.plots.plots.Plot method) (rnavigate.plots.Profile method) (rnavigate.plots.profile.Profile method) (rnavigate.plots.QC method) (rnavigate.plots.qc.QC method) (rnavigate.plots.ROC method) (rnavigate.plots.roc.ROC method) (rnavigate.plots.Skyline method) (rnavigate.plots.skyline.Skyline method) (rnavigate.plots.SM method) (rnavigate.plots.sm.SM method) (rnavigate.plots.SS method) (rnavigate.plots.ss.SS method)

set_indices() (rnavigate.data.PDB method) (rnavigate.data.pdb.PDB method) set_labels() (rnavigate.plots.Profile method) (rnavigate.plots.profile.Profile method) (rnavigate.plots.Skyline method) (rnavigate.plots.skyline.Skyline method) set_multiple_sequence_alignment() (in module rnavigate.data) (in module rnavigate.data.alignments) set_nt_ticks() (in module rnavigate.plots) (in module rnavigate.plots.functions) (in module rnavigate.plots.functions.functions) SHAPEJuMP (class in rnavigate.data) (class in rnavigate.data.interactions) SHAPEMaP (class in rnavigate.data) (class in rnavigate.data.profile) Skyline (class in rnavigate.plots) (class in rnavigate.plots.skyline) SM (class in rnavigate.plots) (class in rnavigate.plots.sm) SS (class in rnavigate.plots) (class in rnavigate.plots.ss) structure structure2 StructureAlignment (class in rnavigate.data) (class in rnavigate.data.alignments) StructureAsInteractions (class in rnavigate.data) (class in rnavigate.data.interactions) StructureCompareMany (class in rnavigate.data) (class in rnavigate.data.interactions) StructureCompareTwo (class in rnavigate.data) (class in rnavigate.data.interactions) StructureCoordinates (class in rnavigate.data) (class in rnavigate.data.secondary_structure)

T

Transcript (class in rnavigate.transcriptomics) (class in rnavigate.transcriptomics.transcriptome) Transcriptome (class in rnavigate.transcriptomics) (class in rnavigate.transcriptomics.transcriptome)

transform_coordinates() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method)

U

update_annotation() (rnavigate.analysis.Fragmapper method) (rnavigate.analysis.fragmapper.Fragmapper method) (rnavigate.analysis.fragmapper.FragmapperReplicates method) (rnavigate.analysis.FragmapperReplicates method)

update_mask() (rnavigate.data.Interactions method) (rnavigate.data.interactions.Interactions method)

V

values_to_hexcolors() (rnavigate.data.colors.ScalarMappable method) (rnavigate.data.ScalarMappable method)

W

WindowedAUROC (class in rnavigate.analysis) (class in rnavigate.analysis.auroc) winsorize() (rnavigate.data.Profile method) (rnavigate.data.profile.Profile method) write_bpp2seq_file() (rnavigate.data.profile.SHAPEMaP method) (rnavigate.data.SHAPEMaP method) write_ct() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) write_cte() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method)

write_dbn() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method) write_fasta() (rnavigate.analysis.check_sequence.SequenceChecker method) (rnavigate.analysis.SequenceChecker method) (rnavigate.data.data.Sequence method) (rnavigate.data.Sequence method) write_shape_file() (rnavigate.data.profile.SHAPEMaP method) (rnavigate.data.SHAPEMaP method) write_sto() (rnavigate.data.secondary_structure.SecondaryStructure method) (rnavigate.data.SecondaryStructure method)

X

xcoordinates (rnavigate.data.secondary_structure.SecondaryStructure property) (rnavigate.data.SecondaryStructure property)

Y

ycoordinates (rnavigate.data.secondary_structure.SecondaryStructure property) (rnavigate.data.SecondaryStructure property)