Index

A

a (Coverage property) accession_to_info() (EUtilsTools method) adapters (in module sequana.resources.data) add_code_section() (SequanaBaseModule method) add_command() (ChromosomeCoverageModule method) add_file() (ITOL method) add_flag_section() (BAMQCModule method) add_float_right() (SequanaBaseModule method) add_fotorama() (SequanaBaseModule method) add_gi_to_header() (ENADownload method) add_images_section() (BAMQCModule method) add_locus_in_fasta() (SnpEff method) AIC() (in module sequana.criteria) AICc() (in module sequana.criteria)

Alignment (class in sequana.bamtools) alpha (RNADiffResults property) (RNADiffTable property) annotate() (Volcano method) annotation_file (SequanaCoverage property) ANOVA (class in sequana.viz.anova) anova() (ANOVA method) anscombe() (VST static method) append_existing_database() (Taxonomy method) as_dict() (Alignment method) (Cigar method) as_sequence() (Cigar method) as_tuple() (Cigar method) AT_skew (DNA property) attributes (GFF3 property)

B

BAI BAM (class in sequana.bamtools) bam_analysis_to_json() (SAMBAMbase method) bam_to_mapped_unmapped_fastq() (in module sequana.tools) BAMQCModule (class in sequana.modules_report.bamqc) BAMSimul (class in sequana.pacbio) Barcoding (class in sequana.pacbio) barplot() (KEGGPathwayEnrichment method) (StatsFile method) (VCF_freebayes method) barplot_count_ORF_CDS_by_frame() (DNA method) barplot_per_sample() (StatsFile method) barplot_summary() (StatsFile method)

barplot_up_and_down() (KEGGPathwayEnrichment method) basic_stats() (ChromosomeCoverageModule method) BED bed (ChromosomeCov property) BED (class in sequana.bed) begin_end_repeat_position (Repeats property) BIC() (in module sequana.criteria) BOC (ChromosomeCov property) boxplot_classified_vs_read_length() (KrakenResults method) boxplot_mapq_concordance() (PacbioMappedBAM method) boxplot_qualities() (SAMBAMbase method) boxplot_quality() (FastQC method) boxplot_read_length_vs_passes() (PacbioSubreads method) build_kmer() (in module sequana.kmer) BUSCO (class in sequana.assembly)

C

C3 (ChromosomeCov property) C4 (ChromosomeCov property) CanuScanner (class in sequana.canu_scanner) check() (MetropolisHasting method) (Sequence method) check_and_save_input_tables() (RNADiffAnalysis method) check_comparisons() (RNADiffAnalysis method) check_condition() (RNADesign method) ChromosomeCov (class in sequana.bedtools) ChromosomeCoverageModule (class in sequana.modules_report.coverage) Cigar (class in sequana.cigar) cigarstring (Cigar attribute) circular (SequanaCoverage property) clean_gff_line_special_characters() (GFF3 method) cluster_probes() (RiboDesigner method) clustering_needed() (RiboDesigner method) Clustermap (class in sequana.viz.heatmap) CNVnator (class in sequana.cnv) Codon (class in sequana.codon) codons (Codon attribute) column_method (Heatmap property) column_metric (Heatmap property) columns (Filtered_freebayes property) comments (FastA property) comparisons (RNADesign property) complement() (Sequence method) compress() (Cigar method) compute_enrichment() (GSEA method) (KEGGPathwayEnrichment method) (PantherEnrichment method)

compute_zscore() (ChromosomeCov method) conditions (RNADesign property) Contigs (class in sequana.contigs) ContigsBase (class in sequana.contigs) copy() (DoubleThresholds method) copy_file() (SequanaBaseModule method) Corrplot (class in sequana.viz.corrplot) count_lines() (FastQ method) count_reads() (FastQ method) Coverage (class in sequana.coverage) coverage_barplot() (ChromosomeCoverageModule method) coverage_plot() (ChromosomeCoverageModule method) CoverageModule (class in sequana.modules_report.coverage) CRAM (class in sequana.bamtools) create_chromosome_reports() (CoverageModule method) create_chromosome_table() (CoverageModule method) create_combobox() (SequanaBaseModule method) create_datatable() (DataTable method) create_embedded_png() (SequanaBaseModule method) create_files_for_rnadiff() (GFF3 method) create_hide_section() (SequanaBaseModule method) create_html() (SequanaBaseModule method) create_javascript_function() (DataTable method) (DataTableFunction method) create_link() (SequanaBaseModule method) create_report_content() (BAMQCModule method) (ChromosomeCoverageModule method) create_taxonomy_file() (NCBITaxonomy method) CS (class in sequana.bamtools) CV (ChromosomeCov property)

D

dataset (Mart property) DataTable (class in sequana.utils.datatables_js) datatable_columns (DataTableFunction property) datatable_options (DataTableFunction property) DataTableFunction (class in sequana.utils.datatables_js) df (BAMSimul property) (ChromosomeCov property) (Contigs property) (Corrplot attribute) (DataTable property) (FeatureCount property) (Filtered_freebayes property) (GFF3 property) (Heatmap property) (IEM property) (KrakenResults property) (PacbioSubreads property)

df_shustring (Repeats property) diagnostics() (MetropolisHasting method) DNA (class in sequana.sequence) do_merge (Repeats property) DOC (ChromosomeCov property) DoubleThresholds (class in sequana.bedtools) download() (KrakenDownload method) download_assembly_report() (NCBIDownload method) download_fasta() (ENADownload method) download_fasta_and_genbank() (in module sequana.snpeff) download_genomes_from_ncbi() (NCBIDownload method) download_ncbi_refseq_release() (NCBIDownload method) download_taxdump() (NCBITaxonReader method) download_taxonomic_file() (Taxonomy method) DSRC

E

EM (class in sequana.mixture) ena_id_to_gi_number() (ENADownload method) ENADownload (class in sequana.databases) entropy() (DNA method) estimate() (EM method) (GaussianMixtureFitting method) EUtilsTools (class in sequana.databases)

evenness (ChromosomeCov property) evenness() (in module sequana.stats) explode() (FastA method) export() (ITOL method) export_to_csv_bed() (RiboDesigner method) export_to_fasta() (RiboDesigner method) export_to_json() (RiboDesigner method) extract_head() (FastQ method)

F

FASTA FastA (class in sequana.fasta) FastQ (class in sequana.fastq) FastQC (class in sequana.fastq) feature_dict (SequanaCoverage property) FeatureCount (class in sequana.featurecounts) FeatureCountMerger (class in sequana.featurecounts) features (GFF3 property) fetch_by_id() (Taxonomy method) fetch_by_name() (Taxonomy method) fetch_clip() (in module sequana.cigar) fetch_deletion() (in module sequana.cigar) fetch_exon() (in module sequana.cigar) fetch_insertion() (in module sequana.cigar) fetch_intron() (in module sequana.cigar) filter() (FastA method) (FastQ method) (RNADiffTable method)

filter_bool() (BAMSimul method) filter_length() (BAMSimul method) (PacbioSubreads method) filter_mapq() (PacbioMappedBAM method) filter_names_dmp_file() (NCBITaxonReader method) filter_nodes_dmp_file() (NCBITaxonReader method) filter_vcf() (VCF_freebayes method) Filtered_freebayes (class in sequana.freebayes_vcf_filter) filters_params (VCF_freebayes property) find_pathways_by_gene() (KEGGPathwayEnrichment method) find_start_codon_position() (Codon method) find_stop_codon_position() (Codon method) find_taxon() (Taxonomy method) findpos() (in module sequana.misc) Fitting (class in sequana.mixture) format_contigs_denovo() (FastA method) frame (Heatmap property) ftp_url (NCBITaxonReader attribute)

G

G (Coverage property) GaussianMixtureFitting (class in sequana.mixture) GaussianMixtureModel (class in sequana.mixture) GC_content() (FastA method) gc_content() (Sequence method) GC_content_sequence() (FastA method) GC_skew (DNA property) gc_vs_coverage() (ChromosomeCoverageModule method) gc_window_size (SequanaCoverage property) gene_sets (GSEA attribute) generalized_anscombe() (VST static method) get_actg_content() (FastQC method) get_all_probes() (RiboDesigner method) get_args() (DoubleThresholds method) get_attributes() (GFF3 method) get_average_name_per_taxon() (NCBITaxonReader method) get_CDS_exons() (BED method) get_centralness() (ChromosomeCov method) get_children() (Taxonomy method) get_codons_from_fasta_and_gff() (Codon method) get_complement() (Sequence method) get_coverage() (PacbioMappedBAM method) get_data() (PantherEnrichment method) get_data_reads() (StatsFile method) get_df() (MultiKrakenResults method) (MultiKrakenResults2 method) (SAMBAMbase method) get_df_concordance() (SAMBAMbase method) get_duplicated_attributes_per_genetic_type() (GFF3 method) get_estimate_insert_size() (SAMBAMbase method) get_exons() (BED method) get_family() (NCBITaxonReader method) get_fasta() (EUtilsTools method) get_features_dict() (GFF3 method) get_flags() (SAMFlags method) get_flags_as_df() (SAMBAMbase method) get_functional_classification() (PantherEnrichment method) get_gaussians() (ChromosomeCov method) get_gc() (ContigsBase method) get_gc_content() (SAMBAMbase method) get_gc_correlation() (ChromosomeCov method) get_gene_lists() (RNADiffResults method) get_guess() (Fitting method) get_kmer() (in module sequana.kmer) get_length_count() (SAMBAMbase method) get_lengths() (FastQ method) get_lengths_as_dict() (FastA method) get_lineage() (Taxonomy method) get_lineage_and_rank() (Taxonomy method) get_mapped_read_length() (SAMBAMbase method)

get_mapping_stats() (PantherEnrichment method) get_mapq_as_df() (SAMBAMbase method) get_max_gc_correlation() (ChromosomeCov method) get_mean_contig_length() (Coverage method) get_mean_nb_passes() (PacbioSubreads method) get_mean_number_contigs() (Coverage method) get_mean_reads_per_contig() (Coverage method) get_meaning() (SAMFlags method) get_most_probable_strand() (in module sequana.featurecounts) get_most_probable_strand_consensus() (in module sequana.featurecounts) get_names_for_given_rank() (Taxonomy method) get_number_of_ccs() (PacbioSubreads method) get_number_taxon() (NCBITaxonReader method) get_occurences() (Sequence method) get_parent_name() (Taxonomy method) get_parent_taxon() (Taxonomy method) get_percent_genome_sequenced() (Coverage method) get_query_end() (SAMBAMbase method) get_query_start() (SAMBAMbase method) get_ranks() (Taxonomy method) get_read_names() (SAMBAMbase method) get_record_for_given_rank() (Taxonomy method) get_required_coverage() (Coverage method) get_reverse() (Sequence method) get_reverse_complement() (Sequence method) get_rna_pos_from_gff() (RiboDesigner method) get_rois() (ChromosomeCov method) get_samflags_count() (SAMBAMbase method) get_samtools_stats_as_df() (SAMBAMbase method) get_scientific_name() (NCBITaxonReader method) get_simplify_dataframe() (GFF3 method) get_stats() (ChromosomeCov method) (FastA method) (FastQC method) (SAMBAMbase method) (SequanaCoverage method) get_stats_full() (SAMBAMbase method) get_summary() (ChromosomeCov method) (Coverage method) get_summary_string() (BUSCO method) get_table() (Coverage method) get_taxon_from_scientific_name() (NCBITaxonReader method) get_taxonomy_db() (KrakenResults method) get_transcript_ranges() (BED method) get_variants() (VCF_freebayes method) getfile() (CanuScanner method) GFF GFF3 (class in sequana.gff3) GSEA (class in sequana.enrichment.gsea) GZLineCounter (class in sequana.tools)

H

hdtr (DoubleThresholds property) header (IEM property) (Repeats property) Heatmap (class in sequana.viz.heatmap) heatmap() (RNADiffResults method) heatmap_vst_centered_data() (RNADiffResults method) high (DoubleThresholds property) high2 (DoubleThresholds property) hinton() (in module sequana.viz.hinton) Hist2D (class in sequana.viz.hist2d) hist_cnvs() (TRF method) hist_concordance() (PacbioMappedBAM method) hist_coverage() (SAMBAMbase method) hist_entropy() (TRF method) hist_event_size() (CNVnator method) hist_GC() (BAMSimul method) (PacbioMappedBAM method) (PacbioSubreads method) hist_length_repeats() (Repeats method) hist_length_repetition() (TRF method) hist_mean_polymerase_read_length() (Barcoding method)

hist_median_ccs() (PacbioMappedBAM method) hist_nb_passes() (PacbioSubreads method) hist_ORF_CDS_linearscale() (DNA method) hist_ORF_CDS_logscale() (DNA method) hist_period_size() (TRF method) hist_plot_contig_length() (Contigs method) hist_polymerase_per_barcode() (Barcoding method) hist_quality_per_barcode() (Barcoding method) hist_read_length() (BAMSimul method) (CanuScanner method) (PacbioMappedBAM method) (PacbioSubreads method) hist_read_length2() (CanuScanner method) hist_repet_by_sequence() (TRF method) hist_snr() (PacbioSubreads method) hist_soft_clipping() (SAMBAMbase method) hist_trimming_read_length() (CanuScanner method) histo_classified_vs_read_length() (KrakenResults method) histogram_gc_content() (FastQC method) histogram_sequence_lengths() (FastQC method) html_id (DataTable property) (DataTableFunction property)

I

Identifier (class in sequana.fastq) IEM (class in sequana.iem) import_tables() (RNADiffResults method) Imshow (class in sequana.viz.imshow) imshow_anova_pairs() (ANOVA method) include_svg_image() (SequanaBaseModule method) index_adapters (IEM property) infer_strandness() (SAMBAMbase method) init() (ChromosomeCov method) (NCBITaxonReader method)

init_roi_datatable() (CoverageModule method) input_filename (SequanaCoverage property) instrument (IEM property) inverse_anscombe() (VST static method) is_fastq() (in module sequana.fastq) is_joint (VCF_freebayes property) is_paired (SAMBAMbase property) is_sorted (SAMBAMbase property) ITOL (class in sequana.itol)

J

joining() (FastQ method)

JSON

K

k (Fitting property) keep_conditions() (RNADesign method) KEGGPathwayEnrichment (class in sequana.enrichment.kegg) kraken_to_csv() (KrakenResults method) kraken_to_json() (KrakenResults method) kraken_to_krona() (KrakenResults method)

KrakenAnalysis (class in sequana.kraken.analysis) KrakenDB (class in sequana.kraken.analysis) KrakenDownload (class in sequana.kraken.analysis) KrakenPipeline (class in sequana.kraken.analysis) KrakenResults (class in sequana.kraken.analysis) KrakenSequential (class in sequana.kraken.analysis)

L

L (Coverage property) launch_snpeff() (SnpEff method) ldtr (DoubleThresholds property) length (Repeats property) lengths (FastA property) list_len_repeats (Repeats property)

load_records() (Taxonomy method) log2_fc (RNADiffResults property) (RNADiffTable property) log_likelihood() (GaussianMixtureModel method) longest_shustring (Repeats property) low (DoubleThresholds property) low2 (DoubleThresholds property)

M

MACS3Reader (class in sequana.macs3) manhattan_plot() (VCF_freebayes method) Mart (class in sequana.enrichment.mart) mean_quality (Quality property) merge() (PeakConsensus method) method (GaussianMixtureFitting property) MetropolisHasting (class in sequana.mh) model (Fitting property) Module module sequana.assembly sequana.bamtools sequana.bed sequana.bedtools sequana.canu_scanner sequana.cigar sequana.cnv sequana.codon sequana.compare sequana.contigs sequana.coverage sequana.criteria sequana.databases sequana.datatools sequana.demultiplex sequana.enrichment sequana.enrichment.gsea sequana.enrichment.kegg sequana.enrichment.mart sequana.enrichment.ontology sequana.enrichment.panther sequana.enrichment.plot_go_terms sequana.enrichment.uniprot_enrichment sequana.fasta sequana.fastq sequana.featurecounts sequana.freebayes_vcf_filter sequana.gff3 sequana.iem sequana.itol sequana.kmer sequana.kraken.analysis sequana.kraken.multikraken sequana.macs3 sequana.mh sequana.misc sequana.mixture sequana.modules_report.bamqc sequana.modules_report.base_module sequana.modules_report.coverage sequana.pacbio sequana.phred sequana.resources.data sequana.ribodesigner sequana.rnadiff sequana.running_median sequana.sequence sequana.sniffer sequana.snpeff sequana.stats sequana.taxonomy sequana.tools sequana.trf sequana.utils.datatables_js sequana.viz.anova sequana.viz.corrplot sequana.viz.heatmap sequana.viz.hinton sequana.viz.hist2d sequana.viz.imshow sequana.viz.pca sequana.viz.scatter sequana.viz.venn sequana.viz.volcano sequana.vst

moving_average() (ChromosomeCov method) (in module sequana.stats) mRNA_inner_distance() (SAMBAMbase method) MultiFeatureCount (class in sequana.featurecounts) MultiKrakenResults (class in sequana.kraken.multikraken) MultiKrakenResults2 (class in sequana.kraken.multikraken)

N

N (Coverage property) n_lines (FastQ property) n_reads (FastQ property) name (IEM property) names (FastA property) (Repeats property) NCBIDownload (class in sequana.databases)

NCBITaxonomy (class in sequana.taxonomy) NCBITaxonReader (class in sequana.databases) next() (ChromosomeCov method) (FastA method) (FastQ method) normalized_coverage() (ChromosomeCoverageModule method) normpdf() (in module sequana.misc)

O

Ontology (class in sequana.enrichment.ontology)

order() (Corrplot method) ORF_pos (DNA property)

P

PacbioMappedBAM (class in sequana.pacbio) PacbioSubreads (class in sequana.pacbio) PantherEnrichment (class in sequana.enrichment.panther) params (Corrplot attribute) pattern (Cigar attribute) PBSim (class in sequana.pacbio) PCA (class in sequana.viz.pca) pdf() (GaussianMixtureModel method) PeakConsensus (class in sequana.macs3) pie_plot() (BUSCO method) plot() (Clustermap method) (CNVnator method) (Corrplot method) (EM method) (Fitting method) (Heatmap method) (Hist2D method) (Imshow method) (KrakenResults method) (PCA method) (Quality method) (Repeats method) (ScatterHist method) (Volcano method) plot2() (KrakenResults method) plot_acgt_content() (FastQC method) plot_all_skews() (DNA method) plot_and_save_all() (Barcoding method) plot_bar_flags() (SAMBAMbase method) plot_bar_mapq() (SAMBAMbase method) plot_boxplot_normeddata() (RNADiffResults method) plot_boxplot_rawdata() (RNADiffResults method) plot_common_major_counts() (RNADiffCompare method) plot_contig_length_vs_GC() (ContigsBase method) plot_contig_length_vs_nreads() (Contigs method) plot_correction_check1() (CanuScanner method) plot_corrplot_counts_normed() (RNADiffCompare method) plot_corrplot_counts_raw() (RNADiffCompare method) plot_count_per_sample() (RNADiffResults method) plot_coverage() (ChromosomeCov method) (SAMBAMbase method) plot_dendogram() (RNADiffResults method) plot_density() (RNADiffResults method) plot_dispersion() (RNADiffResults method) plot_feature_most_present() (RNADiffResults method)

plot_foldchange() (RNADiffCompare method) plot_gc_content() (SAMBAMbase method) plot_GC_read_len() (BAMSimul method) (PacbioMappedBAM method) (PacbioSubreads method) plot_gc_vs_coverage() (ChromosomeCov method) plot_geneset() (RNADiffCompare method) plot_genesets_hist() (KEGGPathwayEnrichment method) plot_hist_coverage() (ChromosomeCov method) plot_hist_normalized_coverage() (ChromosomeCov method) plot_hist_zscore() (ChromosomeCov method) plot_indel_dist() (SAMBAMbase method) plot_insert_size() (SAMBAMbase method) plot_isomap() (RNADiffResults method) plot_jaccard_distance() (RNADiffCompare method) plot_kmer() (CanuScanner method) plot_mds() (RNADiffResults method) plot_most_expressed_features() (RNADiffResults method) plot_padj_hist() (RNADiffTable method) plot_pca() (RNADiffResults method) plot_pca_vs_max_features() (PCA method) plot_percentage_null_read_counts() (RNADiffResults method) plot_piechart() (PantherEnrichment method) plot_polymerase_per_barcode() (Barcoding method) plot_pvalue_hist() (RNADiffTable method) plot_read_length() (SAMBAMbase method) plot_rois() (ChromosomeCov method) plot_scatter_contig_length_vs_nreads_cov() (Contigs method) plot_stacked_hist() (MultiKrakenResults method) (MultiKrakenResults2 method) plot_strandness() (MultiFeatureCount method) plot_subreads_histogram() (Barcoding method) plot_unknown_barcodes() (StatsFile method) plot_upset() (RNADiffResults method) plot_venn() (in module sequana.viz.venn) (PeakConsensus method) plot_venn_all() (RNADiffCompare method) plot_venn_down() (RNADiffCompare method) plot_venn_up() (RNADiffCompare method) plot_volcano() (MACS3Reader method) (RNADiffCompare method) (RNADiffTable method) plot_volcano_differences() (RNADiffCompare method) plotly_hist_read_length() (SAMBAMbase method) png_to_embedded_png() (SequanaBaseModule method) proba_to_quality_sanger() (in module sequana.phred)

Q

Quality (class in sequana.phred) quality (Quality property)

quality_to_proba_sanger() (in module sequana.phred) query() (Mart method) quick_fix() (IEM method)

R

random_selection() (PacbioSubreads method) read() (GFF3 method) read_and_save_selected_features() (GFF3 method) read_annot() (RNADiffResults method) read_csv() (RNADiffResults method) record (Variant property) reference_file (SequanaCoverage property) regions_of_interest() (ChromosomeCoverageModule method) Repeats (class in sequana.sequence) report() (RNADiffResults method) reset() (BAMSimul method) (PacbioMappedBAM method) (PacbioSubreads method) (SAMBAMbase method) resume (Variant property) reverse() (Sequence method) reverse_and_save() (FastA method) reverse_complement() (Sequence method) rewind() (FastQ method) (VCF_freebayes method) RiboDesigner (class in sequana.ribodesigner)

RNA (class in sequana.sequence) RNADesign (class in sequana.rnadiff) RNADiffAnalysis (class in sequana.rnadiff) RNADiffCompare (class in sequana.compare) RNADiffResults (class in sequana.rnadiff) RNADiffTable (class in sequana.rnadiff) rois (ChromosomeCov property) row_method (Heatmap property) row_metric (Heatmap property) run() (ChromosomeCov method) (KrakenAnalysis method) (KrakenPipeline method) (KrakenSequential method) (PBSim method) (RiboDesigner method) (RNADiffAnalysis method) (RunningMedian method) runmean() (in module sequana.stats) running_median() (ChromosomeCov method) (in module sequana.running_median) RunningMedian (class in sequana.running_median)

S

SAM (class in sequana.bamtools) SAMBAMbase (class in sequana.bamtools) SAMFlags (class in sequana.bamtools) samples (IEM property) (Variant property) (VCF_freebayes property) save() (Mart method) save_annotation_to_csv() (GFF3 method) save_chart() (PantherEnrichment method) save_collapsed_fasta() (FastA method) save_core_genomes() (BUSCO method) save_ctg_to_fasta() (FastA method) save_gff_filtered() (GFF3 method) save_pathway() (KEGGPathwayEnrichment method) save_pathways() (KEGGPathwayEnrichment method) save_project() (KEGGPathwayEnrichment method) save_significant_pathways() (KEGGPathwayEnrichment method) save_summary() (PacbioSubreads method) scan_correction() (CanuScanner method) scan_trimming() (CanuScanner method) scandata() (TRF method) scatter_length_cov_gc() (ContigsBase method) scatter_plot() (BUSCO method) ScatterHist (class in sequana.viz.scatter) scatterplot() (KEGGPathwayEnrichment method) score (BUSCO property) search() (NCBITaxonReader method) select_random_reads() (FastA method) (FastQ method) select_reads() (FastQ method) sequana.assembly module sequana.bamtools module sequana.bed module sequana.bedtools module sequana.canu_scanner module sequana.cigar module sequana.cnv module sequana.codon module sequana.compare module sequana.contigs module sequana.coverage module sequana.criteria module sequana.databases module sequana.datatools module sequana.demultiplex module sequana.enrichment module sequana.enrichment.gsea module sequana.enrichment.kegg module sequana.enrichment.mart module sequana.enrichment.ontology module sequana.enrichment.panther module sequana.enrichment.plot_go_terms module sequana.enrichment.uniprot_enrichment module sequana.fasta module sequana.fastq module sequana.featurecounts module sequana.freebayes_vcf_filter module sequana.gff3 module sequana.iem module sequana.itol module sequana.kmer module sequana.kraken.analysis module sequana.kraken.multikraken module sequana.macs3 module

sequana.mh module sequana.misc module sequana.mixture module sequana.modules_report.bamqc module sequana.modules_report.base_module module sequana.modules_report.coverage module sequana.pacbio module sequana.phred module sequana.resources.data module sequana.ribodesigner module sequana.rnadiff module sequana.running_median module sequana.sequence module sequana.sniffer module sequana.snpeff module sequana.stats module sequana.taxonomy module sequana.tools module sequana.trf module sequana.utils.datatables_js module sequana.viz.anova module sequana.viz.corrplot module sequana.viz.heatmap module sequana.viz.hinton module sequana.viz.hist2d module sequana.viz.imshow module sequana.viz.pca module sequana.viz.scatter module sequana.viz.venn module sequana.viz.volcano module sequana.vst module sequana_data() (in module sequana.datatools) SequanaBaseModule (class in sequana.modules_report.base_module) SequanaCoverage (class in sequana.bedtools) Sequence (class in sequana.sequence) sequence (Sequence property) sequences (FastA property) set_gene_lists() (RNADiffTable method) set_links_to_column() (DataTableFunction method) set_overlap_filtering() (CanuScanner method) set_read_correction() (CanuScanner method) set_tooltips_to_column() (DataTableFunction method) settings (IEM property) show() (KrakenPipeline method) simulate() (MetropolisHasting method) Snakefile sniffer() (in module sequana.sniffer) SnpEff (class in sequana.snpeff) split_chunks() (FastQ method) split_lines() (FastQ method) stats (PacbioSubreads property) stats() (Cigar method) (Contigs method) (FastQ method) (Sequence method) StatsBAM2Mapped (class in sequana.tools) StatsFile (class in sequana.demultiplex) STD (ChromosomeCov property) stride() (PacbioSubreads method) subcoverage() (ChromosomeCoverageModule method) summary (SAMBAMbase property) summary() (BUSCO method) (FastA method) (PacbioSubreads method) (RNADiffResults method) (RNADiffTable method)

T

target_distribution() (PBSim method) taxon (PantherEnrichment property) Taxonomy (class in sequana.taxonomy) taxons (KrakenResults property) template (RNADiffAnalysis attribute) textwrap() (in module sequana.misc) threshold (DNA property) (Repeats property) to_bed() (GFF3 method) (PeakConsensus method) to_csv() (ChromosomeCov method) (Filtered_freebayes method) (RNADiffResults method) to_fasta() (BAMSimul method) (FastA method) (FastQ method) (GFF3 method) (IEM method) (PacbioMappedBAM method) (PacbioSubreads method)

to_fastq() (BAMSimul method) (PacbioMappedBAM method) (PacbioSubreads method) (SAMBAMbase method) to_gtf() (GFF3 method) to_html() (StatsBAM2Mapped method) to_igv_chrom_size() (FastA method) to_js() (KrakenResults method) to_json() (StatsBAM2Mapped method) to_kmer_content() (FastQ method) to_krona() (FastQ method) to_paf() (SAMBAMbase method) to_saf() (PeakConsensus method) to_summary_reads() (StatsFile method) to_tsv() (FeatureCountMerger method) to_vcf() (Filtered_freebayes method) transcript_to_gene_mapping() (GFF3 method) TRF (class in sequana.trf) type_filter (DNA property) type_window (DNA property) types (Cigar attribute)

U

upload() (ITOL method)

V

validate() (IEM method) Variant (class in sequana.freebayes_vcf_filter) variants (Filtered_freebayes property) VCF vcf (Filtered_freebayes property)

VCF_freebayes (class in sequana.freebayes_vcf_filter) version (IEM property) (KrakenDB property) Volcano (class in sequana.viz.volcano) VST (class in sequana.vst)

W

wget() (in module sequana.misc)

window (DNA property) window_size (SequanaCoverage property)

X

Xtarget (MetropolisHasting property)

Y

YAML	Ytarget (MetropolisHasting property)

Z

zscore_distribution() (ChromosomeCoverageModule method)