Index Symbols | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z Symbols --add-CDS-and-mRNA sequana-gff command line option --annotation-attribute sequana-enrichment-kegg command line option sequana-enrichment-panther command line option sequana-enrichment-uniprot command line option --annotation-file sequana-rnadiff command line option --attribute sequana-salmon-cli command line option --attribute-name sequana-rnadiff command line option --attributes sequana-biomart command line option --bam-file sequana-find-integrated-genes command line option --batch sequana-rnadiff command line option --beta-prior sequana-rnadiff command line option --biomart sequana-enrichment-kegg command line option --buffer-size sequana-fastq-split command line option --by-part sequana-fastq-split command line option --by-size sequana-fastq-split command line option --check sequana-samplesheet command line option --chromosomes sequana-somy-score command line option sequana-telomark command line option --chunk-size sequana-telomark command line option --comparison sequana-enrichment-kegg command line option --comparisons sequana-rnadiff command line option --compute-levels sequana-enrichment-panther command line option sequana-enrichment-uniprot command line option --condition sequana-enrichment-kegg command line option sequana-enrichment-panther command line option sequana-enrichment-uniprot command line option sequana-rnadiff command line option --cooks-cutoff sequana-rnadiff command line option --count-reads sequana-fastq command line option --count-sequences sequana-fasta command line option --dataset sequana-biomart command line option --design sequana-rnadiff command line option --dry-run sequana-lane-merging command line option --estimated-diploy-coverage sequana-somy-score command line option --exclude-chromosomes sequana-somy-score command line option --explode sequana-fasta command line option --extract sequana-fasta command line option --extract-adapters sequana-samplesheet command line option --fast sequana-somy-score command line option --feature sequana-salmon-cli command line option --feature-name sequana-rnadiff command line option --features sequana-gff-to-light-gff command line option sequana-rnadiff command line option --file1 sequana-mapping command line option sequana-rnaseq-compare command line option --file2 sequana-mapping command line option sequana-rnaseq-compare command line option --fit-type sequana-rnadiff command line option --flag sequana-somy-score command line option --force sequana-lane-merging command line option sequana-ribodesigner command line option sequana-rnadiff command line option --force-clustering sequana-ribodesigner command line option --forward-depth sequana-html-report command line option --freebayes-score sequana-html-report command line option --frequency sequana-html-report command line option --full-check sequana-samplesheet command line option --gene-id sequana-gff command line option --gff sequana-salmon-cli command line option --gzip sequana-fastq-split command line option --head sequana-fastq command line option --host sequana-biomart command line option --hover-name sequana-rnadiff command line option --identity-step sequana-ribodesigner command line option --independent-filtering sequana-rnadiff command line option --input sequana-g4hunter command line option sequana-gtf-fixer command line option sequana-salmon-cli command line option --input-gff sequana-variants-comparison command line option --input-vcf sequana-variants-comparison command line option --keep-all-conditions sequana-rnadiff command line option --keep-polymorphic sequana-html-report command line option --kegg-background sequana-enrichment-kegg command line option --kegg-name sequana-enrichment-kegg command line option --kegg-pathways-directory sequana-enrichment-kegg command line option --lanes sequana-lane-merging command line option --log2-foldchange-cutoff sequana-enrichment-kegg command line option sequana-enrichment-panther command line option sequana-enrichment-uniprot command line option --logger sequana-biomart command line option sequana-blast-to-gff command line option sequana-embl-to-fasta command line option sequana-enrichment-kegg command line option sequana-enrichment-panther command line option sequana-enrichment-uniprot command line option sequana-feature-counts command line option sequana-find-integrated-genes command line option sequana-gff-to-gtf command line option sequana-gff-to-light-gff command line option sequana-rnadiff command line option sequana-rnaseq-compare command line option sequana-somy-score command line option sequana-taxonomy command line option sequana-telomark command line option sequana-variants-comparison command line option --mapq sequana-somy-score command line option --mart sequana-biomart command line option --max-enriched-go-terms sequana-enrichment-panther command line option sequana-enrichment-uniprot command line option --max-genes sequana-enrichment-panther command line option sequana-enrichment-uniprot command line option --max-n-probes sequana-ribodesigner command line option --max-pathways sequana-enrichment-kegg command line option --merge sequana-fasta command line option sequana-fastq command line option --method sequana-ribodesigner command line option sequana-somy-score command line option --min-depth sequana-html-report command line option --minimum-depth sequana-somy-score command line option --minimum-mean-reads-per-condition-per-gene sequana-rnadiff command line option --minimum-mean-reads-per-gene sequana-rnadiff command line option --model sequana-rnadiff command line option --module sequana-summary command line option --name sequana-find-integrated-genes command line option --no-beta-prior sequana-rnadiff command line option --no-compute-levels sequana-enrichment-panther command line option sequana-enrichment-uniprot command line option --no-force sequana-rnadiff command line option --no-independent-filtering sequana-rnadiff command line option --no-keep-all-conditions sequana-rnadiff command line option --no-shrinkage sequana-rnadiff command line option --no-split-full-table sequana-rnadiff command line option --ontologies sequana-enrichment-panther command line option sequana-enrichment-uniprot command line option --ordered-sample sequana-variants-comparison command line option --output sequana-biomart command line option sequana-fasta command line option sequana-fastq command line option sequana-feature-counts command line option sequana-g4hunter command line option sequana-gff command line option sequana-gtf-fixer command line option sequana-salmon-cli command line option sequana-samplesheet command line option --output-csv-file sequana-html-report command line option --output-directory sequana-enrichment-kegg command line option sequana-enrichment-panther command line option sequana-enrichment-uniprot command line option sequana-html-report command line option sequana-lane-merging command line option sequana-ribodesigner command line option sequana-rnadiff command line option --output-file sequana-summary command line option --output-html sequana-variants-comparison command line option --output-image sequana-ribodesigner command line option --output-json sequana-summary command line option --output-vcf-file sequana-html-report command line option --pacbio sequana-mapping command line option --padj-cutoff sequana-enrichment-kegg command line option sequana-enrichment-panther command line option sequana-enrichment-uniprot command line option --panther-taxon sequana-enrichment-panther command line option --pattern sequana-fastq-split command line option sequana-feature-counts command line option sequana-lane-merging command line option --peak-height sequana-telomark command line option --peak-width sequana-telomark command line option --plot-linearx sequana-enrichment-kegg command line option sequana-enrichment-panther command line option sequana-enrichment-uniprot command line option --plot-style sequana-telomark command line option --quality-threshold sequana-variants-comparison command line option --quick-fix sequana-samplesheet command line option --reference sequana-mapping command line option sequana-rnadiff command line option --remove-sample sequana-variants-comparison command line option --report-only sequana-rnadiff command line option --reverse-complement sequana-fasta command line option --reverse-depth sequana-html-report command line option --save-contig-name sequana-fasta command line option --save-reads sequana-find-integrated-genes command line option --score sequana-g4hunter command line option --search-kegg sequana-taxonomy command line option --search-panther sequana-taxonomy command line option --seq-type sequana-ribodesigner command line option --shrinkage sequana-rnadiff command line option --slurm-queue sequana-lane-merging command line option --split-full-table sequana-rnadiff command line option --strand-ratio sequana-html-report command line option --tag sequana-find-integrated-genes command line option sequana-telomark command line option --tail sequana-fastq command line option --taxon sequana-enrichment-uniprot command line option --telomeric-span sequana-somy-score command line option --threads sequana-lane-merging command line option sequana-mapping command line option sequana-ribodesigner command line option sequana-somy-score command line option --title sequana-variants-comparison command line option --to-chrom-size sequana-fasta command line option --use-sambamba sequana-lane-merging command line option sequana-mapping command line option --version sequana command line option --window sequana-g4hunter command line option --window-size sequana-somy-score command line option --xticks-fontsize sequana-rnadiff command line option -1 sequana-mapping command line option -2 sequana-mapping command line option -a sequana-salmon-cli command line option -F sequana-salmon-cli command line option -f sequana-salmon-cli command line option -g sequana-variants-comparison command line option -i sequana-g4hunter command line option sequana-gtf-fixer command line option sequana-salmon-cli command line option sequana-variants-comparison command line option -k sequana-somy-score command line option -o sequana-fasta command line option sequana-fastq command line option sequana-g4hunter command line option sequana-gff command line option sequana-gtf-fixer command line option sequana-lane-merging command line option sequana-salmon-cli command line option sequana-variants-comparison command line option -p sequana-mapping command line option -q sequana-variants-comparison command line option -r sequana-mapping command line option sequana-variants-comparison command line option -s sequana-lane-merging command line option sequana-mapping command line option sequana-variants-comparison command line option -t sequana-mapping command line option sequana-variants-comparison command line option A a (Coverage property) adapters (in module sequana.resources.data) add_adapters_section() (CutadaptModule method) add_annotation_Ld1S() (OrthoFinder method) add_blast_section() (KrakenModule method) add_CDS_and_mRNA() (GFF3 method) add_cluster() (RNAdiffModule method) add_code_section() (SequanaBaseModule method) add_command() (ChromosomeCoverageModule method) add_diagnostics_section() (KrakenModule method) add_directon_index() (GFF3 method) add_dispersion() (RNAdiffModule method) add_file() (ITOL method) add_flag_section() (BAMQCModule method) add_float_right() (SequanaBaseModule method) add_fotorama() (SequanaBaseModule method) add_go() (ModulePantherEnrichment method) (ModuleUniprotEnrichment method) add_histogram_section() (CutadaptModule method) add_images_section() (BAMQCModule method) (TRFModule method) add_individual_report() (RNAdiffModule method) add_info() (TRFModule method) add_intergenic_regions() (GFF3 method) add_intro_download() (VariantCallingModule method) add_kegg() (ModuleKEGGEnrichment method) add_locus_in_fasta() (SnpEff method) add_log_section() (CutadaptModule method) add_main_section() (FastQCModule method) add_normalisation() (RNAdiffModule method) add_overview() (VariantCallingModule method) add_params() (Summary method) add_plot_count_per_sample() (RNAdiffModule method) add_png() (PacbioInputBAMModule method) add_regions_and_save_gff() (GFF3 method) add_section() (MultiSummary method) add_stat_section() (CutadaptModule method) add_stats() (BWABAMtoFastQModule method) (FastQStatsModule method) (PacbioInputBAMModule method) (PhixModule method) add_summary_section() (CutadaptModule method) (KrakenModule method) add_table() (TRFModule method) add_table_results_hierarchy_section() (KrakenModule method) add_table_results_section() (KrakenModule method) add_upset_plot() (RNAdiffModule method) AIC() (in module sequana.criteria) AICc() (in module sequana.criteria) Alignment (class in sequana.bamtools) all_consensus() (ConsensusBuilder method) alpha (RNADiffResults property) (RNADiffTable property) annotate() (Volcano method) annotate_gff() (PfamDomtblout method) annotation_file (SequanaCoverage property) ANOVA (class in sequana.viz.anova) anova() (ANOVA method) anscombe() (VST static method) apply_variants() (in module sequana.variants) Apptainer Aragorn (class in sequana.annotation) as_dict() (Alignment method) (Cigar method) (Summary method) as_sequence() (Cigar method) as_tuple() (Cigar method) AT_skew (DNA 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) (VariantFile method) barplot_count_ORF_CDS_by_frame() (DNA method) barplot_per_sample() (StatsFile method) barplot_summary() (StatsFile method) barplot_up_and_down() (KEGGPathwayEnrichment method) base_score() (G4Hunter method) basic_stats() (ChromosomeCoverageModule method) BED bed (ChromosomeCov property) BED (class in sequana.bed) begin_end_repeat_position (Repeats property) best_hit_per_query() (BLAST method) BIC() (in module sequana.criteria) BinaryPercentage (class in sequana.viz.plotly) BLAST (class in sequana.blast) blast_to_gff() (in module sequana.blast) BOC (ChromosomeCov property) bootstrap() (Kozak method) Boxplot (class in sequana.viz.boxplot) boxplot() (SomyScore method) boxplot_classified_vs_read_length() (KrakenResults method) boxplot_mapq_concordance() (PacbioMappedBAM method) boxplot_qualities() (SAMBAMbase method) boxplot_quality() (FastQC method) (MGI method) boxplot_read_length_vs_passes() (PacbioSubreads method) build_csv() (KEGGHelper method) build_kmer() (in module sequana.kmer) build_reference() (LAA_Assembly method), [1] builddata() (KozakAddon method) BUSCO (class in sequana.assembly) BWABAMtoFastQModule (class in sequana.modules_report.bwa_bam_to_fastq) by_part() (FastqSplitter method) by_size() (FastqSplitter method) C C3 (ChromosomeCov property) C4 (ChromosomeCov property) calculate_mfe() (in module sequana.rnafold) caller() (SequanaReport method) CanuScanner (class in sequana.canu_scanner) CanvasBar (class in sequana.viz.bar) CanvasJS (class in sequana.plots.canvasjs_base) CanvasJSLineGraph (class in sequana.plots.canvasjs_linegraph) check() (MetropolisHasting method) (Sequence method) check_and_save_input_tables() (RNADiffAnalysis method) check_comparisons() (RNADiffAnalysis method) check_method() (Linkage method) check_metric() (Linkage method) Checker (class in sequana.utils.checker) checker() (RNADesign method) (SampleSheet method) CheckM (class in sequana.checkm) ChromosomeCov (class in sequana.bedtools) ChromosomeCoverageModule (class in sequana.modules_report.coverage) chromosomes (VariantFile property) CIGAR Cigar (class in sequana.cigar) cigarstring (Cigar property) circular (SequanaCoverage property) circular_shifts() (in module sequana.telomere) clean_gff_line_special_characters() (GFF3 method) clear_sequence_cache() (FastA method) Cluster (class in sequana.viz.clusterisation) cluster_names_to_bed() (GFF3 method) cluster_probes() (RiboDesigner method) clustering_needed() (RiboDesigner method) Clustermap (class in sequana.viz.heatmap) CMSearchParser (class in sequana.annotation) CNVnator (class in sequana.cnv) Codon (class in sequana.codon) codons (Codon attribute) collapse_first_cds (Kozak property) column_method (Heatmap property) column_metric (Heatmap property) comments (FastA property) comparisons (RNADesign property) complement() (Sequence method) compress() (Cigar method) compute_bendability() (in module sequana.metrics) compute_coverage() (SomyScore method) compute_cpg_content() (in module sequana.cpg_islands) compute_enrichment() (GSEA method) (KEGGPathwayEnrichment method) (PantherEnrichment method) compute_fisher_strand_filter() (in module sequana.vcftools) compute_frequency() (in module sequana.vcftools) compute_helix_twist() (in module sequana.metrics) compute_melting_temperature_salt_adjusted() (in module sequana.biomol) compute_melting_temperature_wallace_rule() (in module sequana.biomol) compute_strand_balance() (in module sequana.vcftools) compute_W50() (KLAnalysis method) compute_zscore() (ChromosomeCov method) Conda environment conditions (RNADesign property) Consensus (class in sequana.laa) (class in sequana.pacbio_amplicon) ConsensusBuilder (class in sequana.kozak) contig_names (GFF3 property) Contigs (class in sequana.contigs) contigs (VariantFile property) ContigsBase (class in sequana.contigs) copy() (DoubleThresholds method) copy_file() (SequanaBaseModule method) cor() (Phantom 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) CpG() (in module sequana.cpg_islands) CRAM (class in sequana.bamtools) create_canvas_js_object() (CanvasJS method) create_canvasjs() (CanvasJSLineGraph method) create_chromosome_reports() (CoverageModule method) create_chromosome_table() (CoverageModule method) create_combobox() (SequanaBaseModule method) create_command_section() (RNAdiffModule method) create_datatable() (DataTable method) (JointCallingModule method) create_div_chart_container() (CanvasJS method) create_embedded_png() (SequanaBaseModule method) create_hide_section() (SequanaBaseModule method) create_histogram_frequencies() (VariantCallingModule method) create_histogram_frequencies2() (VariantCallingModule method) create_html() (SequanaBaseModule method) create_individual_reports() (RNAdiffModule method) create_javascript_function() (DataTable method) (DataTableFunction method) create_link() (SequanaBaseModule method) create_main_report_content() (RNAdiffModule method) create_report_content() (BAMQCModule method) (BWABAMtoFastQModule method) (ChromosomeCoverageModule method) (CutadaptModule method) (FastQCModule method) (FastQStatsModule method) (KrakenModule method) (ModuleKEGGEnrichment method) (ModulePantherEnrichment method) (ModuleUniprotEnrichment method) (MultiSummary method) (PacbioInputBAMModule method) (PhixModule method) (SequanaReport method) (TRFModule method) (VariantCallingModule method) create_summary_barplot() (CoverageModule method) create_taxonomy_file() (NCBITaxonomy method) Cruciforms (class in sequana.cruciforms) CS (class in sequana.bamtools) CutadaptModule (class in sequana.modules_report.cutadapt) CV (ChromosomeCov property) D data_description (Summary property) 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) date (Summary property) DEG Dendogram (class in sequana.viz.dendogram) dependencies() (SequanaReport method) (SummaryBase method) df (BAMSimul property) (ChromosomeCov property) (Contigs property) (Corrplot attribute) (DataTable property) (Dendogram property) (FeatureCount property) (FilteredVariantFile property) (GFF3 property) (Heatmap property) (KozakAddon property) (KrakenResults property) (MPileup property) (PacbioSubreads property) (SampleSheet property) (SomyScore property) (VariantFile property) df2html() (in module sequana.utils.df2html) df_shustring (Repeats property) diagnostics() (MetropolisHasting method) directon_to_bed() (GFF3 method) directons (GFF3 property) display_filename_prefix_last (DisplayablePath attribute) display_filename_prefix_middle (DisplayablePath attribute) display_parent_prefix_last (DisplayablePath attribute) display_parent_prefix_middle (DisplayablePath attribute) displayable() (DisplayablePath method) DisplayablePath (class in sequana.utils.tree) displayname (DisplayablePath property) DNA (class in sequana.sequence) do_merge (Repeats property) DOC (ChromosomeCov property) dotplot_from_lastz() (in module sequana.viz.dotplot) DoubleThresholds (class in sequana.bedtools) download() (in module sequana.misc) (KrakenDownload method) download_fasta_and_genbank() (in module sequana.snpeff) download_taxonomic_file() (Taxonomy method) DSRC E EM (class in sequana.mixture) entropy (Motif property) entropy() (DNA method) entropy_distribution_by_period() (TRF method) estimate() (EM method) (GaussianMixtureFitting method) evenness (ChromosomeCov property) evenness() (in module sequana.stats) expected_data_headers (SampleSheet attribute) expected_headers_fields (SampleSheet attribute) explode() (FastA method) export() (ITOL method) export_all_probes_to_fasta() (RiboDesigner method) export_meme() (Kozak method) export_to_csv_bed() (RiboDesigner method) export_to_json() (RiboDesigner method) extract() (RFAMSplitter method) extract_fasta() (GenBank method) extract_head() (FastQ method) F factorize_sequences() (in module sequana.telomere) FASTA sequana-ribodesigner command line option FastA (class in sequana.fasta) FASTA_FILE sequana-telomark command line option FastaGFFCorrection (class in sequana.fasta_gff_correction) FASTQ FastQ (class in sequana.fastq) FastQC (class in sequana.fastq) (class in sequana.fastqc) FastQCModule (class in sequana.modules_report.fastqc) FastqSplitter (class in sequana.fastq_splitter) FastQStatsModule (class in sequana.modules_report.fastq_stats) feature_dict (SequanaCoverage property) FeatureCount (class in sequana.featurecounts) FeatureCountMerger (class in sequana.featurecounts) features (GenBank property) (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) FILENAME sequana-fasta command line option sequana-fastq command line option sequana-gff command line option sequana-somy-score command line option filter() (FastA method) (FastQ method) (RNADiffTable method) filter_bool() (BAMSimul method) filter_dataframe() (Kozak method) filter_length() (BAMSimul method) (PacbioSubreads method) filter_mapq() (PacbioMappedBAM method) filter_vcf() (VariantFile method) FilteredVariantFile (class in sequana.variants) filters_information() (VariantCallingModule method) find_gaps() (FastA method) find_kmers() (KozakAddon method) find_LHS_telomere() (Telomere method) find_motif() (in module sequana.find_motif) find_motif_bam() (FindMotif method) find_motif_fasta() (FindMotif method) find_motif_from_sequence() (FindMotif method) find_pathways_by_gene() (KEGGPathwayEnrichment method) find_representative_kmers() (Telomere method) find_restriction_sites() (in module sequana.restriction) find_RHS_telomere() (Telomere method) find_start_codon_position() (Codon method) (FastaGFFCorrection method) find_stop_codon_position() (Codon method) find_taxon() (Taxonomy method) FindMotif (class in sequana.find_motif) findpos() (in module sequana.misc) fisher_exact() (in module sequana.utils.fisher) Fitting (class in sequana.mixture) fix() (GTFFixer method) fix_and_save_fasta() (FastaGFFCorrection method) fix_and_save_gff() (FastaGFFCorrection method) format_contigs_denovo() (FastA method) frame (Dendogram property) (Heatmap property) FRiP (class in sequana.frip) G G (Coverage property) G4Hunter (class in sequana.G4hunter) G4HunterReader (class in sequana.G4hunter) 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) GenBank (class in sequana.genbank) genbank_features_parser() (GenBank method) gene_sets (GSEA attribute) generalized_anscombe() (VST static method) genetic_type (Kozak property) GeneTrees (class in sequana.orthofinder) get_actg_content() (FastQC method) get_adapters_percent() (MultiSummary method) (ReadSummary method) get_all_kmer_counts() (KozakAddon method) get_all_kmer_counts_by_chromosome() (KozakAddon method) get_all_kmer_counts_genes_only() (KozakAddon method) get_all_probes() (RiboDesigner method) get_all_start_codons() (FastaGFFCorrection method) get_all_stop_codons() (FastaGFFCorrection method) get_args() (DoubleThresholds method) get_attributes() (GFF3 method) get_average_read_length() (ReadSummary method) get_bases() (Consensus method), [1] 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_consensus() (ConsensusBuilder method) get_coverage() (PacbioMappedBAM method) get_cumulative_sum() (FastA method) get_cutadapt_stats() (ReadSummary method) get_data() (Kozak method) (PantherEnrichment method) (Phantom method) get_data_reads() (StatsFile method) get_df() (MultiKrakenResults method) (MultiKrakenResults2 method) (SAMBAMbase method) get_df_concordance() (SAMBAMbase method) get_dinucleotide_count() (DNA method) get_dna_flexibility() (DNA method) get_duplicated_attributes_per_genetic_type() (GFF3 method) get_duplicated_attributes_per_genetic_type2() (GFF3 method) get_entropy() (DNA method) get_estimate_insert_size() (SAMBAMbase method) get_exons() (BED method) get_fastq_stats_samples() (ReadSummary method) get_feature_counts() (Salmon method) get_feature_counts_eukaryotes() (Salmon method) get_feature_counts_prokaryotes() (Salmon method) get_features_dict() (GFF3 method) get_file() (IsoSeqQC method) get_flags() (SAMFlags method) get_flags_as_df() (SAMBAMbase method) get_functional_classification() (PantherEnrichment method) get_G4() (G4Hunter method) get_gaussians() (ChromosomeCov method) get_gc() (ContigsBase method) get_gc_content() (SAMBAMbase method) get_gc_content_samples() (MultiSummary method) get_gc_correlation() (ChromosomeCov method) get_gc_per_chromosome() (Kozak method) get_gene_lists() (RNADiffResults method) get_go_description() (QuickGOGraph method) get_guess() (Fitting method) get_homopolymers() (DNA method) get_html() (HTMLDirectory method) get_html_table() (ModulePantherEnrichment method) (ModuleUniprotEnrichment method) get_III() (KLAnalysis method) get_information_content() (Kozak method) get_informational_entropy() (DNA method) get_intergenic_regions() (GFF3 method) get_karlin_signature_difference() (DNA method) get_kmer() (in module sequana.kmer) get_kmer_counts() (KozakAddon method) get_KSI() (KLAnalysis method) 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_mean_contig_length() (Coverage method) get_mean_nb_passes() (PacbioSubreads method) get_mean_number_contigs() (Coverage method) get_mean_quality_samples() (MultiSummary method) (ReadSummary 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_mutation() (MPileup method) get_names_for_given_rank() (Taxonomy method) get_nreads() (FastqSplitter method) get_nreads_raw() (MultiSummary method) (ReadSummary method) get_number_of_ccs() (PacbioSubreads method) get_occurences() (Sequence method) get_odd_ratio() (KozakAddon method) get_output_total_reads() (MultiSummary method) (ReadSummary method) get_parent_name() (Taxonomy method) get_parent_taxon() (Taxonomy method) get_peak_position() (KLAnalysis method) get_peak_position_and_length() (Repeats method) get_peak_strength() (KLAnalysis method) get_percent_genome_sequenced() (Coverage method) get_phix_percent() (MultiSummary method) (ReadSummary method) get_population() (Consensus method), [1] get_power() (KLAnalysis method) get_projects() (MultiSummary method) get_PTU() (GFF3 method) get_query_end() (SAMBAMbase method) get_query_length() (Cigar method) get_query_start() (SAMBAMbase method) get_random_contexts() (Kozak method) get_ranks() (Taxonomy method) get_read1_with_adapters_percent() (ReadSummary method) get_read2_with_adapters_percent() (ReadSummary method) get_read_names() (SAMBAMbase method) get_records_for_given_rank() (Taxonomy method) get_reference_length() (Cigar method) get_repeats_in_region() (TRF 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_seqid2size() (GFF3 method) get_signal_concentration() (KLAnalysis method) get_simplify_dataframe() (GFF3 method) get_sliding_kmer_count_five_to_three_prime() (Telomere method) get_sliding_kmer_count_three_to_five_prime() (Telomere method) get_statistics() (Sequence method) get_stats() (ChromosomeCov method) (FastA method) (FastQC method) (FastQStatsModule 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) (ModuleKEGGEnrichment method) get_table_dependencies() (SummaryBase method) get_table_versions() (SequanaReport method) get_taxonomy_db() (KrakenResults method) get_total_errors() (MPileup method) get_total_information() (KLAnalysis method) get_transcript_ranges() (BED method) get_trimming_percent() (MultiSummary method) (ReadSummary method) get_trinucleotide_count() (DNA method) get_types() (GenBank method) get_unique_names() (MultiSummary method) get_urls() (MultiSummary method) get_variant_type() (VariantFile method) getfile() (CanuScanner method) GFA (class in sequana.gfa) GFF sequana-ribodesigner command line option GFF3 (class in sequana.gff3) GFF_FILENAME sequana-gff-to-gtf command line option GSEA (class in sequana.enrichment.gsea) GTF GTFFixer (class in sequana.gtf_fixer) GZLineCounter (class in sequana.tools) H hdtr (DoubleThresholds property) header (Repeats property) (SampleSheet 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) hist2D() (in module sequana.viz.vizir) hist_amplicon() (LAA method), [1] hist_average_quality() (IsoSeqQC method) 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_gene_counts() (OrthoFinder method) hist_length_repeats() (Repeats method) hist_length_repetition() (TRF method) hist_long_read() (FastQ 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_passes() (IsoSeqBAM 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) (IsoSeqBAM method) (PacbioMappedBAM method) (PacbioSubreads method) hist_read_length2() (CanuScanner method) hist_read_length_consensus_isoform() (IsoSeqQC method) hist_repetitions_per_sequence() (TRF method) hist_score() (VariantFile 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) Homer (class in sequana.homer) html_id (DataTable property) (DataTableFunction property) HTMLDirectory (class in sequana.utils.tree) I Identifier (class in sequana.fastq) identify_deletions() (Consensus method), [1] Ideogram (class in sequana.viz.ideogram) IDR (class in sequana.idr) IDR2score() (IDR method) IEM (class in sequana.iem) IMotif (class in sequana.imotif) import_tables() (RNADiffResults method) Imshow (class in sequana.viz.imshow) imshow_anova_pairs() (ANOVA method) include_start_codon (Kozak property) include_svg_image() (SequanaBaseModule method) index_adapters (SampleSheet property) infer_strandness() (SAMBAMbase method) information_content (Motif property) init() (ChromosomeCov method) init_roi_datatable() (CoverageModule method) initialize_matrix() (in module sequana.rnafold) INPUT sequana-gff-to-light-gff command line option INPUT_BLAST sequana-blast-to-gff command line option INPUT_EMBL sequana-embl-to-fasta command line option INPUT_FASTQ sequana-fastq-split command line option input_filename (SequanaCoverage property) instrument (SampleSheet property) inverse_anscombe() (VST static method) is_complementary() (in module sequana.rnafold) is_cruciform() (Cruciforms method) is_fastq() (in module sequana.fastq) is_joint (VariantFile property) is_paired (SAMBAMbase property) is_palindrome() (Palindromes method) is_sorted (SAMBAMbase property) is_telomeric() (Telomere method) is_tRNA_or_ribosomal() (GFF3 method) Isomap (class in sequana.viz.isomap) IsoSeqBAM (class in sequana.isoseq) IsoSeqQC (class in sequana.isoseq) ITOL (class in sequana.itol) J joining() (FastQ method) JointCallingModule (class in sequana.modules_report.joint_calling) JSON K k (Fitting property) k-mer keep_ATG_only (Kozak property) keep_conditions() (RNADesign method) keep_reads() (FastQ method) KEGGHelper (class in sequana.kegg) KEGGPathwayEnrichment (class in sequana.enrichment.kegg) kl_vs_random_atg() (Kozak method) KLAnalysis (class in sequana.kozak) Kozak (class in sequana.kozak) kozak_weight_score() (in module sequana.kozak) KozakAddon (class in sequana.kozak) KozakWeightScore (class in sequana.kozak) kraken_to_csv() (KrakenResults method) kraken_to_json() (KrakenResults method) kraken_to_krona() (KrakenResults method) KrakenAnalysis (class in sequana.kraken.analysis) KrakenConsensus (class in sequana.kraken.consensus) KrakenDB (class in sequana.kraken.analysis) KrakenDownload (class in sequana.kraken.downloads) KrakenModule (class in sequana.modules_report.kraken) KrakenPipeline (class in sequana.kraken.analysis) KrakenResults (class in sequana.kraken.analysis) KrakenSequential (class in sequana.kraken.sequential) KronaMerger (class in sequana.krona) L L (Coverage property) LAA (class in sequana.laa) (class in sequana.pacbio_amplicon) LAA_Assembly (class in sequana.laa) (class in sequana.pacbio_amplicon) launch_snpeff() (SnpEff method) ldtr (DoubleThresholds property) left_kozak (Kozak property) lempel_ziv_complexity() (in module sequana.metrics) length (Repeats property) lengths (FastA property) (IsoSeqBAM property) lgamma() (in module sequana.utils.fisher) Linkage (class in sequana.viz.linkage) linkage() (Linkage method) list_len_repeats (Repeats property) load_files() (G4HunterReader method) load_merged_data() (G4HunterReader method) load_records() (Taxonomy method) load_records_from_csv() (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) make_tree() (DisplayablePath class method) manhattan_plot() (VariantFile method) Mart (class in sequana.enrichment.mart) mean_quality (Quality property) merge() (PeakConsensus method) method (Dendogram property) (GaussianMixtureFitting property) methods (Linkage attribute) metric (Dendogram property) metrics (Linkage attribute) MetropolisHasting (class in sequana.mh) MGI (class in sequana.mgi) mlnTest2l() (in module sequana.utils.fisher) mlnTest2r() (in module sequana.utils.fisher) mlnTest2t() (in module sequana.utils.fisher) mode (IDR property) model (Fitting property) Module module sequana.annotation sequana.assembly sequana.bamtools sequana.bed sequana.bedtools sequana.biomol sequana.blast sequana.canu_scanner sequana.checkm sequana.cigar sequana.cnv sequana.codon sequana.compare sequana.contigs sequana.coverage sequana.cpg_islands sequana.criteria sequana.cruciforms sequana.datatools sequana.demultiplex sequana.enrichment.gsea sequana.enrichment.kegg sequana.enrichment.mart sequana.enrichment.ontology sequana.enrichment.panther sequana.enrichment.plot_go_terms sequana.enrichment.quickgo sequana.enrichment.uniprot_enrichment sequana.fasta sequana.fasta_gff_correction sequana.fastq sequana.fastq_splitter sequana.fastqc sequana.featurecounts sequana.find_motif sequana.freebayes_vcf_filter sequana.frip sequana.G4hunter sequana.genbank sequana.gfa sequana.gff3 sequana.gtf_fixer sequana.hmmtools sequana.homer sequana.idr sequana.iem sequana.imotif sequana.isoseq sequana.itol sequana.kegg sequana.kmer sequana.kozak sequana.kraken.analysis sequana.kraken.consensus sequana.kraken.downloads sequana.kraken.multikraken sequana.kraken.sequential sequana.krona sequana.laa sequana.macs3 sequana.metrics sequana.mgi sequana.mh sequana.misc sequana.mixture sequana.modules_report.bamqc sequana.modules_report.base_module sequana.modules_report.bwa_bam_to_fastq sequana.modules_report.coverage sequana.modules_report.cutadapt sequana.modules_report.fastq_stats sequana.modules_report.fastqc sequana.modules_report.joint_calling sequana.modules_report.kegg_enrichment sequana.modules_report.kraken sequana.modules_report.multi_summary sequana.modules_report.pacbio_input_bam sequana.modules_report.panther_enrichment sequana.modules_report.phix sequana.modules_report.quast sequana.modules_report.rnadiff sequana.modules_report.summary sequana.modules_report.trf sequana.modules_report.uniprot_enrichment sequana.modules_report.variant_calling sequana.mpileup sequana.orthofinder sequana.pacbio sequana.pacbio_amplicon sequana.palindromes sequana.phantom sequana.phred sequana.plots.canvasjs_base sequana.plots.canvasjs_linegraph sequana.protein sequana.resources.data sequana.restriction sequana.ribodesigner sequana.rnadiff sequana.rnafold sequana.running_median sequana.salmon sequana.sequence sequana.sniffer sequana.snpeff sequana.somy sequana.stats sequana.summary sequana.taxonomy sequana.telomere sequana.tools sequana.trf sequana.utils.checker sequana.utils.config sequana.utils.datatables_js sequana.utils.df2html sequana.utils.fisher sequana.utils.pandas sequana.utils.singleton sequana.utils.tree sequana.variants sequana.vcftools sequana.viz.anova sequana.viz.bar sequana.viz.boxplot sequana.viz.clusterisation sequana.viz.core sequana.viz.corrplot sequana.viz.dendogram sequana.viz.dotplot sequana.viz.heatmap sequana.viz.hinton sequana.viz.hist2d sequana.viz.ideogram sequana.viz.imshow sequana.viz.isomap sequana.viz.linkage sequana.viz.mds sequana.viz.pca sequana.viz.plotly sequana.viz.scatter sequana.viz.tsne sequana.viz.venn sequana.viz.vizir sequana.viz.volcano sequana.vst sequana.wigtools sequana.zdna ModuleKEGGEnrichment (class in sequana.modules_report.kegg_enrichment) ModulePantherEnrichment (class in sequana.modules_report.panther_enrichment) ModuleUniprotEnrichment (class in sequana.modules_report.uniprot_enrichment) Motif (class in sequana.kozak) moving_average() (ChromosomeCov method) (in module sequana.stats) MPileup (class in sequana.mpileup) mRNA_inner_distance() (SAMBAMbase method) MultiCheckM (class in sequana.checkm) MultiFeatureCount (class in sequana.featurecounts) MultiKrakenResults (class in sequana.kraken.multikraken) MultiKrakenResults2 (class in sequana.kraken.multikraken) multiple_downloads() (in module sequana.misc) MultiQC MultiSummary (class in sequana.modules_report.multi_summary) N N (Coverage property) n_lines (FastQ property) n_reads (FastQ property) N_significant_peaks (IDR property) NAME sequana-html-report command line option sequana-samplesheet command line option sequana-summary command line option name (Summary property) names (FastA property) (Repeats property) NCBITaxonomy (class in sequana.taxonomy) next() (ChromosomeCov method) (FastA method) (FastQ method) NGS normalized_coverage() (ChromosomeCoverageModule method) normpdf() (in module sequana.misc) O Ontology (class in sequana.enrichment.ontology) order() (Corrplot method) ORF_pos (DNA property) OrthoFinder (class in sequana.orthofinder) OrthoGroups (class in sequana.orthofinder) OUTPUT sequana-gff-to-light-gff command line option OUTPUT_FASTA sequana-embl-to-fasta command line option OUTPUT_GFF sequana-blast-to-gff command line option P PacbioInputBAMModule (class in sequana.modules_report.pacbio_input_bam) PacbioMappedBAM (class in sequana.pacbio) PacbioSubreads (class in sequana.pacbio) PAFReader (class in sequana.annotation) Palindromes (class in sequana.palindromes) PandasReader (class in sequana.utils.pandas) PantherEnrichment (class in sequana.enrichment.panther) params (Corrplot attribute) parse() (MultiSummary method) parse_aragorn_output() (Aragorn method) parse_atropos() (CutadaptModule method) parse_cutadapt() (CutadaptModule method) passes (IsoSeqBAM property) pattern (Cigar attribute) PBSim (class in sequana.pacbio) PCA (class in sequana.viz.pca) pdf() (GaussianMixtureModel method) PeakConsensus (class in sequana.macs3) PfamDomtblout (class in sequana.hmmtools) Phantom (class in sequana.phantom) PhantomPeaksReader (class in sequana.phantom) PhixModule (class in sequana.modules_report.phix) pie_annotation() (Homer method) pie_plot() (BUSCO method) pieplot() (VariantFile method) plot() (Boxplot method) (Clustermap method) (CNVnator method) (Corrplot method) (Dendogram method) (EM method) (Fitting method) (FRiP method) (Heatmap method) (Hist2D method) (Ideogram method) (Imshow method) (Isomap method) (KrakenResults method) (PCA method) (Quality method) (Repeats method) (ScatterHist method) (TSNE method) (Volcano method) plot2() (KrakenResults method) plot_acgt() (MGI method) plot_acgt_content() (FastQC method) plot_alignment() (FindMotif method) plot_all_skews() (DNA method) plot_and_save_all() (Barcoding method) plot_bar_flags() (SAMBAMbase method) plot_bar_mapq() (SAMBAMbase method) plot_barplot() (ModuleKEGGEnrichment method) plot_barplot_up_and_down() (ModuleKEGGEnrichment method) plot_boxplot_normeddata() (RNADiffResults method) plot_boxplot_rawdata() (RNADiffResults method) plot_common_major_counts() (RNADiffCompare method) plot_contig() (Telomere 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_count_versus_length() (TRF method) plot_coverage() (ChromosomeCov method) (SAMBAMbase method) plot_cumulated() (KozakAddon method) plot_dendogram() (RNADiffResults method) plot_density() (RNADiffResults method) plot_dispersion() (RNADiffResults method) plot_entropy() (Motif method) plot_feature_most_present() (RNADiffResults method) plot_filter_stats() (SomyScore method) plot_foldchange() (RNADiffCompare method) plot_frequency() (VariantFile method) plot_gc_content() (SAMBAMbase method) plot_GC_per_chromosome() (Kozak method) plot_GC_read_len() (BAMSimul method) (FastQ 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_horizontal_bar() (BinaryPercentage method) plot_idr_vs_peaks() (IDR method) plot_indel_dist() (SAMBAMbase method) plot_information_content() (Motif method) plot_insert_size() (SAMBAMbase method) plot_isomap() (RNADiffResults method) plot_jaccard_distance() (RNADiffCompare method) plot_KL_divergence() (Kozak method) plot_kmer() (CanuScanner method) plot_kozak_chi2() (Kozak method) plot_logo() (Kozak method) plot_logo_all_kmers() (KozakAddon method) plot_logo_bits() (Kozak method) plot_logo_purine_pyrimidine() (Kozak method) plot_max_length_amplicon_per_barcode() (LAA method), [1] plot_mds() (RNADiffResults method) plot_most_expressed_features() (RNADiffResults method) plot_motif_logo() (TRF method) plot_mutation_matrix() (MPileup 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_period_vs_CNV() (TRF method) plot_piechart() (PantherEnrichment method) plot_polymerase_per_barcode() (Barcoding method) plot_pvalue_hist() (RNADiffTable method) plot_rank_vs_idr_score() (IDR method) plot_ranks() (IDR method) plot_read_length() (SAMBAMbase method) plot_repeat_density() (TRF method) plot_rois() (ChromosomeCov method) plot_RSC() (PhantomPeaksReader method) plot_scatter() (ModuleKEGGEnrichment method) plot_scatter_contig_length_vs_nreads_cov() (Contigs method) plot_scatter_odds_ratio_annotated() (KozakAddon method) plot_scatter_odds_ratio_gene_vs_genome() (KozakAddon method) plot_scores() (IDR method) plot_sequence_quality() (FastQC method) plot_specific_alignment() (FindMotif method) plot_stack_bars() (MPileup method) plot_stacked_hist() (MultiKrakenResults method) (MultiKrakenResults2 method) plot_strandness() (MultiFeatureCount method) plot_subreads_histogram() (Barcoding method) plot_summary() (Telomere method) plot_total_errors() (MPileup 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) populate_adapters() (MultiSummary method) populate_gc_samples() (MultiSummary method) populate_mean_quality() (MultiSummary method) populate_nreads_raw() (MultiSummary method) populate_output_total_reads() (MultiSummary method) populate_phix() (MultiSummary method) populate_trimming() (MultiSummary method) print_sequence_region_for_gff() (FastA method) proba_to_quality_sanger() (in module sequana.phred) Protein (class in sequana.protein) Q Quality (class in sequana.phred) quality (Quality property) quality_to_proba_sanger() (in module sequana.phred) QuastModule() (in module sequana.modules_report.quast) query() (Mart method) quick_fix() (SampleSheet method) QuickGOGraph (class in sequana.enrichment.quickgo) R RAGTAG (class in sequana.annotation) random_selection() (PacbioSubreads method) read() (GFA method) (GFF3 method) (PfamDomtblout method) (PhantomPeaksReader method) read_align() (Phantom method) read_and_save_selected_features() (GFF3 method) read_annot() (RNADiffResults method) read_csv() (RNADiffResults method) read_data() (CutadaptModule method) read_sample() (FastQC method) ReadSummary (class in sequana.modules_report.multi_summary) reference_file (SequanaCoverage property) regions_of_interest() (ChromosomeCoverageModule method) remove_anomalies() (Phantom method) remove_flanks() (SomyScore method) remove_low_depth() (SomyScore method) remove_outliers() (SomyScore method) Repeats (class in sequana.sequence) report() (RNADiffResults method) reset() (BAMSimul method) (PacbioMappedBAM method) (PacbioSubreads method) (SAMBAMbase method) reverse() (Sequence method) reverse_and_save() (FastA method) reverse_complement() (Sequence method) rewind() (FastQ method) RFAMSplitter (class in sequana.annotation) RiboDesigner (class in sequana.ribodesigner) right_kozak (Kozak property) RNA (class in sequana.sequence) RNADesign (class in sequana.rnadiff) RNADIFF_DIRECTORY sequana-enrichment-kegg command line option sequana-enrichment-panther command line option sequana-enrichment-uniprot command line option RNADiffAnalysis (class in sequana.rnadiff) RNADiffCompare (class in sequana.compare) RNAdiffModule (class in sequana.modules_report.rnadiff) RNADiffResults (class in sequana.rnadiff) RNADiffTable (class in sequana.rnadiff) RNAmmer (class in sequana.annotation) rois (ChromosomeCov property) row_method (Heatmap property) row_metric (Heatmap property) Rule run() (Aragorn method) (ChromosomeCov method) (Consensus method), [1] (Cruciforms method) (G4Hunter method) (IMotif method) (KrakenAnalysis method) (KrakenConsensus method) (KrakenPipeline method) (KrakenSequential method) (Palindromes method) (PBSim method) (Phantom method) (RiboDesigner method) (RNADiffAnalysis method) (RunningMedian method) (Telomere method) (ZDNA method) runmean() (in module sequana.stats) running_median() (ChromosomeCov method) (in module sequana.running_median) RunningMedian (class in sequana.running_median) S Salmon (class in sequana.salmon) SAM (class in sequana.bamtools) SAMBAMbase (class in sequana.bamtools) SAMFlags (class in sequana.bamtools) Sample sheet samples (SampleSheet property) (VariantFile property) SampleSheet (class in sequana.iem) save() (Mart method) save_annotation_to_csv() (GFF3 method) save_as_gff() (GFF3 method) save_chart() (PantherEnrichment method) (QuickGOGraph method) save_collapsed_fasta() (FastA method) save_consensus() (Consensus method), [1] save_core_genomes() (BUSCO method) save_ctg_to_fasta() (FastA method) save_fasta() (LAA_Assembly method), [1] save_feature_counts() (Salmon method) save_gff_filtered() (GFF3 method) save_non_telomeric_reads() (TelomerFilter method) save_pathway() (KEGGPathwayEnrichment method) save_pathways() (KEGGPathwayEnrichment method) save_project() (KEGGPathwayEnrichment method) save_reads() (TelomerFilter method) save_significant_pathways() (KEGGPathwayEnrichment method) save_summary() (PacbioSubreads method) save_telomeric_reads() (TelomerFilter method) scale_data() (Cluster method) scan() (BLAST method) scan_correction() (CanuScanner method) scan_trimming() (CanuScanner method) scatter_length_cov_gc() (ContigsBase method) scatter_plot() (BUSCO method) ScatterHist (class in sequana.viz.scatter) scatterplot() (KEGGPathwayEnrichment method) scc() (Phantom method) score (BUSCO property) score() (KozakWeightScore method) score2IDR() (IDR method) score_batch() (KozakWeightScore method) search() (GFF3 method) (KEGGHelper method) select_random_reads() (FastA method) (FastQ method) select_reads() (FastQ method) sequana command line option --version sequana-biomart command line option --attributes --dataset --host --logger --mart --output sequana-blast-to-gff command line option --logger INPUT_BLAST OUTPUT_GFF sequana-embl-to-fasta command line option --logger INPUT_EMBL OUTPUT_FASTA sequana-enrichment-kegg command line option --annotation-attribute --biomart --comparison --condition --kegg-background --kegg-name --kegg-pathways-directory --log2-foldchange-cutoff --logger --max-pathways --output-directory --padj-cutoff --plot-linearx RNADIFF_DIRECTORY sequana-enrichment-panther command line option --annotation-attribute --compute-levels --condition --log2-foldchange-cutoff --logger --max-enriched-go-terms --max-genes --no-compute-levels --ontologies --output-directory --padj-cutoff --panther-taxon --plot-linearx RNADIFF_DIRECTORY sequana-enrichment-uniprot command line option --annotation-attribute --compute-levels --condition --log2-foldchange-cutoff --logger --max-enriched-go-terms --max-genes --no-compute-levels --ontologies --output-directory --padj-cutoff --plot-linearx --taxon RNADIFF_DIRECTORY sequana-fasta command line option --count-sequences --explode --extract --merge --output --reverse-complement --save-contig-name --to-chrom-size -o FILENAME sequana-fastq command line option --count-reads --head --merge --output --tail -o FILENAME sequana-fastq-split command line option --buffer-size --by-part --by-size --gzip --pattern INPUT_FASTQ sequana-feature-counts command line option --logger --output --pattern sequana-find-integrated-genes command line option --bam-file --logger --name --save-reads --tag sequana-g4hunter command line option --input --output --score --window -i -o sequana-gff command line option --add-CDS-and-mRNA --gene-id --output -o FILENAME sequana-gff-to-gtf command line option --logger GFF_FILENAME sequana-gff-to-light-gff command line option --features --logger INPUT OUTPUT sequana-gtf-fixer command line option --input --output -i -o sequana-html-report command line option --forward-depth --freebayes-score --frequency --keep-polymorphic --min-depth --output-csv-file --output-directory --output-vcf-file --reverse-depth --strand-ratio NAME sequana-lane-merging command line option --dry-run --force --lanes --output-directory --pattern --slurm-queue --threads --use-sambamba -o -s sequana-mapping command line option --file1 --file2 --pacbio --reference --threads --use-sambamba -1 -2 -p -r -s -t sequana-ribodesigner command line option --force --force-clustering --identity-step --max-n-probes --method --output-directory --output-image --seq-type --threads FASTA GFF sequana-rnadiff command line option --annotation-file --attribute-name --batch --beta-prior --comparisons --condition --cooks-cutoff --design --feature-name --features --fit-type --force --hover-name --independent-filtering --keep-all-conditions --logger --minimum-mean-reads-per-condition-per-gene --minimum-mean-reads-per-gene --model --no-beta-prior --no-force --no-independent-filtering --no-keep-all-conditions --no-shrinkage --no-split-full-table --output-directory --reference --report-only --shrinkage --split-full-table --xticks-fontsize sequana-rnaseq-compare command line option --file1 --file2 --logger sequana-salmon-cli command line option --attribute --feature --gff --input --output -a -f -F -i -o sequana-samplesheet command line option --check --extract-adapters --full-check --output --quick-fix NAME sequana-somy-score command line option --chromosomes --estimated-diploy-coverage --exclude-chromosomes --fast --flag --logger --mapq --method --minimum-depth --telomeric-span --threads --window-size -k FILENAME sequana-summary command line option --module --output-file --output-json NAME sequana-taxonomy command line option --logger --search-kegg --search-panther sequana-telomark command line option --chromosomes --chunk-size --logger --peak-height --peak-width --plot-style --tag FASTA_FILE sequana-variants-comparison command line option --input-gff --input-vcf --logger --ordered-sample --output-html --quality-threshold --remove-sample --title -g -i -o -q -r -s -t sequana.annotation module sequana.assembly module sequana.bamtools module sequana.bed module sequana.bedtools module sequana.biomol module sequana.blast module sequana.canu_scanner module sequana.checkm module sequana.cigar module sequana.cnv module sequana.codon module sequana.compare module sequana.contigs module sequana.coverage module sequana.cpg_islands module sequana.criteria module sequana.cruciforms module sequana.datatools module sequana.demultiplex 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.quickgo module sequana.enrichment.uniprot_enrichment module sequana.fasta module sequana.fasta_gff_correction module sequana.fastq module sequana.fastq_splitter module sequana.fastqc module sequana.featurecounts module sequana.find_motif module sequana.freebayes_vcf_filter module sequana.frip module sequana.G4hunter module sequana.genbank module sequana.gfa module sequana.gff3 module sequana.gtf_fixer module sequana.hmmtools module sequana.homer module sequana.idr module sequana.iem module sequana.imotif module sequana.isoseq module sequana.itol module sequana.kegg module sequana.kmer module sequana.kozak module sequana.kraken.analysis module sequana.kraken.consensus module sequana.kraken.downloads module sequana.kraken.multikraken module sequana.kraken.sequential module sequana.krona module sequana.laa module sequana.macs3 module sequana.metrics module sequana.mgi module sequana.mh module sequana.misc module sequana.mixture module sequana.modules_report.bamqc module sequana.modules_report.base_module module sequana.modules_report.bwa_bam_to_fastq module sequana.modules_report.coverage module sequana.modules_report.cutadapt module sequana.modules_report.fastq_stats module sequana.modules_report.fastqc module sequana.modules_report.joint_calling module sequana.modules_report.kegg_enrichment module sequana.modules_report.kraken module sequana.modules_report.multi_summary module sequana.modules_report.pacbio_input_bam module sequana.modules_report.panther_enrichment module sequana.modules_report.phix module sequana.modules_report.quast module sequana.modules_report.rnadiff module sequana.modules_report.summary module sequana.modules_report.trf module sequana.modules_report.uniprot_enrichment module sequana.modules_report.variant_calling module sequana.mpileup module sequana.orthofinder module sequana.pacbio module sequana.pacbio_amplicon module sequana.palindromes module sequana.phantom module sequana.phred module sequana.plots.canvasjs_base module sequana.plots.canvasjs_linegraph module sequana.protein module sequana.resources.data module sequana.restriction module sequana.ribodesigner module sequana.rnadiff module sequana.rnafold module sequana.running_median module sequana.salmon module sequana.sequence module sequana.sniffer module sequana.snpeff module sequana.somy module sequana.stats module sequana.summary module sequana.taxonomy module sequana.telomere module sequana.tools module sequana.trf module sequana.utils.checker module sequana.utils.config module sequana.utils.datatables_js module sequana.utils.df2html module sequana.utils.fisher module sequana.utils.pandas module sequana.utils.singleton module sequana.utils.tree module sequana.variants module sequana.vcftools module sequana.viz.anova module sequana.viz.bar module sequana.viz.boxplot module sequana.viz.clusterisation module sequana.viz.core module sequana.viz.corrplot module sequana.viz.dendogram module sequana.viz.dotplot module sequana.viz.heatmap module sequana.viz.hinton module sequana.viz.hist2d module sequana.viz.ideogram module sequana.viz.imshow module sequana.viz.isomap module sequana.viz.linkage module sequana.viz.mds module sequana.viz.pca module sequana.viz.plotly module sequana.viz.scatter module sequana.viz.tsne module sequana.viz.venn module sequana.viz.vizir module sequana.viz.volcano module sequana.vst module sequana.wigtools module sequana.zdna module sequana_data() (in module sequana.datatools) SequanaBaseModule (class in sequana.modules_report.base_module) SequanaCoverage (class in sequana.bedtools) SequanaReport (class in sequana.modules_report.summary) Sequence (class in sequana.sequence) sequence (Sequence property) sequences (FastA property) set_axis_x() (CanvasJSLineGraph method) set_axis_y() (CanvasJSLineGraph method) set_axis_y2() (CanvasJSLineGraph method) set_context() (Kozak method) set_data() (CanvasJS method) set_GC_to_AT_mutations() (MPileup method) set_gene_lists() (RNADiffTable method) set_legend() (CanvasJS method) set_links_to_column() (DataTableFunction method) set_options() (CanvasJS method) set_overlap_filtering() (CanuScanner method) set_read_correction() (CanuScanner method) set_title() (CanvasJS method) set_tooltips_to_column() (DataTableFunction method) settings (SampleSheet property) simulate() (MetropolisHasting method) Singleton (class in sequana.utils.singleton) Snakefile Snakemake sniffer() (in module sequana.sniffer) SnpEff (class in sequana.snpeff) SomyScore (class in sequana.somy) sorted_mixed_names (FastA property) sorted_names (FastA property) split_according_to_reference_name() (Consensus method) split_chunks() (FastQ method) split_lines() (FastQ method) split_records() (RFAMSplitter method) stacked_bar() (in module sequana.viz.bar) stats (PacbioSubreads property) stats() (Cigar method) (Contigs method) (FastQ method) (IsoSeqBAM method) (IsoSeqQC method) (Phantom method) (Sequence method) StatsBAM2Mapped (class in sequana.tools) StatsFile (class in sequana.demultiplex) STD (ChromosomeCov property) strand_ratio() (in module sequana.vcftools) stride() (PacbioSubreads method) subcoverage() (ChromosomeCoverageModule method) Summary (class in sequana.summary) summary (SAMBAMbase property) summary() (BUSCO method) (FastA method) (ModuleKEGGEnrichment method) (ModulePantherEnrichment method) (ModuleUniprotEnrichment method) (OrthoFinder method) (OrthoGroups method) (PacbioSubreads method) (RNAdiffModule method) (RNADiffResults method) (RNADiffTable method) (TRF method) SummaryBase (class in sequana.modules_report.summary) T target_distribution() (PBSim method) Taxon taxon (PantherEnrichment property) Taxonomy (class in sequana.taxonomy) taxons (KrakenResults property) Telomere (class in sequana.telomere) TelomerFilter (class in sequana.telomere) template (RNADiffAnalysis attribute) temporary_lr() (Kozak method) test_both() (in module sequana.utils.fisher) test_left() (in module sequana.utils.fisher) test_right() (in module sequana.utils.fisher) textwrap() (in module sequana.misc) threshold (DNA property) (Repeats property) to_bed() (Cruciforms method) (G4HunterReader method) (GFF3 method) (IMotif method) (Palindromes method) (PeakConsensus method) (TRF method) (ZDNA method) to_bedgraph() (TRF method) to_csv() (ChromosomeCov method) (FilteredVariantFile method) (RNADiffResults method) to_fasta() (BAMSimul method) (FastA method) (FastQ method) (GFF3 method) (PacbioMappedBAM method) (PacbioSubreads method) (SampleSheet method) to_fastq() (BAMSimul method) (PacbioMappedBAM method) (PacbioSubreads method) (SAMBAMbase method) to_gff() (PfamDomtblout method) to_gff3() (RNAmmer method) to_gtf() (GFF3 method) to_html() (CanvasBar method) (StatsBAM2Mapped method) to_igv_chrom_size() (FastA method) to_js() (KrakenResults method) to_json() (StatsBAM2Mapped method) (Summary method) to_kmer_content() (FastQ method) to_krona() (FastQ method) to_paf() (SAMBAMbase method) to_pep() (GFF3 method) to_saf() (PeakConsensus method) to_summary() (IsoSeqQC method) to_summary_reads() (StatsFile method) to_tsv() (FeatureCountMerger method) (KronaMerger method) to_vcf() (FilteredVariantFile method) (VariantFile method) to_wig() (Repeats method) top_motifs() (TRF method) transcript_to_gene_mapping() (GFF3 method) TRF (class in sequana.trf) TRFModule (class in sequana.modules_report.trf) tryme() (Checker method) TSNE (class in sequana.viz.tsne) type_filter (DNA property) type_window (DNA property) types (Cigar attribute) U upload() (ITOL method) V validate() (RNADesign method) (SampleSheet method) variant_calling() (VariantCallingModule method) VariantCallingModule (class in sequana.modules_report.variant_calling) VariantFile (class in sequana.variants) variants (FilteredVariantFile property) (VariantFile property) VCF vcf (FilteredVariantFile property) version (KrakenDB property) (SampleSheet property) (Summary property) VizInput2D (class in sequana.viz.core) Volcano (class in sequana.viz.volcano) VST (class in sequana.vst) W wget() (in module sequana.misc) window (DNA property) window_size (SequanaCoverage property) workflow() (SequanaReport method) Wrapper write_sequences() (G4Hunter method) X Xtarget (MetropolisHasting property) Y YAML yield_wig_by_chromosome() (in module sequana.wigtools) Ytarget (MetropolisHasting property) Z ZDNA (class in sequana.zdna) zscore_distribution() (ChromosomeCoverageModule method)
