Index

_

__init__() (PyNCBI.NoDataAvailableError method)

A

abstract (PyNCBI.PMCFullText attribute) (PyNCBI.PubMedArticle attribute) accession (PyNCBI.AssemblyRecord attribute) (PyNCBI.BioProjectRecord attribute) (PyNCBI.BioSampleRecord attribute) (PyNCBI.BlastHit attribute) (PyNCBI.ClinVarRecord attribute) (PyNCBI.DownloadPlan attribute) (PyNCBI.FASTASequence attribute) (PyNCBI.FilePreview attribute) (PyNCBI.GenomeDownloadResult attribute) (PyNCBI.GEOSearchHit attribute) (PyNCBI.InspectionReport attribute) (PyNCBI.NucleotideRecord attribute) AccessionNotFoundError AccessionPrivateError acquire() (PyNCBI.NCBIRealmLimiter method) (PyNCBI.TokenBucketLimiter method) ActivityEvent (class in PyNCBI) ActivityReporter (class in PyNCBI) agent_mode (PyNCBI.Config attribute) AgentEnvelope (class in PyNCBI) aliases (PyNCBI.GeneRecord attribute) align_len (PyNCBI.BlastHit attribute)

allele_frequencies (PyNCBI.DbSNPRecord attribute) alt_alleles (PyNCBI.DbSNPRecord attribute) annotate_gene_ids() (in module PyNCBI) annotate_probes() (in module PyNCBI) annotation_date (PyNCBI.AssemblyRecord attribute) annotation_name (PyNCBI.AssemblyRecord attribute) api_key (PyNCBI.Config attribute) app_config (PyNCBI.NCBIClient property) archive_members (PyNCBI.FilePreview attribute) array_type (PyNCBI.GSM property) assembly_level (PyNCBI.AssemblyRecord attribute) assembly_name (PyNCBI.AssemblyRecord attribute) assembly_status (PyNCBI.AssemblyRecord attribute) assembly_type (PyNCBI.AssemblyRecord attribute) AssemblyRecord (class in PyNCBI) assess_study() (in module PyNCBI) assessed_at (PyNCBI.QualityReport attribute) attach_cache() (PyNCBI.ClientMetrics method) attach_full_text() (in module PyNCBI) attributes (PyNCBI.BioSampleRecord attribute) audit_log_path (PyNCBI.Config attribute) author_details (PyNCBI.PubMedArticle attribute) authors (PyNCBI.PubMedArticle attribute) AUTO (PyNCBI.FetchMode attribute)

B

biomol (PyNCBI.NucleotideRecord attribute) bioproject (PyNCBI.AssemblyRecord attribute) bioproject_id (PyNCBI.GEOSearchHit attribute) (PyNCBI.GSEInfo attribute) (PyNCBI.InspectionReport attribute) (PyNCBI.StudyRecord attribute) BioProjectRecord (class in PyNCBI) biosample (PyNCBI.AssemblyRecord attribute) biosample_url (PyNCBI.GSMInfo attribute) (PyNCBI.InspectionReport attribute)

BioSampleRecord (class in PyNCBI) bit_score (PyNCBI.BlastHit attribute) blast() (in module PyNCBI) BlastHit (class in PyNCBI) BlastJob (class in PyNCBI) BlastResult (class in PyNCBI) BotChallengeError build_study_bundle() (in module PyNCBI) build_study_record() (in module PyNCBI) ByteProgressTracker (class in PyNCBI) bytes_received (PyNCBI.RequestEvent attribute)

C

cache_dir (PyNCBI.MetadataStore property) (PyNCBI.Session property) cache_folder (PyNCBI.Config attribute) CacheCorruptedError CacheError CacheNotFoundError CacheWriteError candidates (PyNCBI.ExpressionResult attribute) canonical_json() (PyNCBI.StudyRecord method) canonical_spdi (PyNCBI.ClinVarRecord attribute) cdna_change (PyNCBI.ClinVarRecord attribute) characteristics (PyNCBI.GSM property) (PyNCBI.GSMInfo attribute) (PyNCBI.InspectionReport attribute) (PyNCBI.SampleRecord attribute) characteristics_summary (PyNCBI.GSE property) (PyNCBI.InspectionReport attribute) characteristics_table (PyNCBI.GSE property) CharacteristicSummary (class in PyNCBI) check_blast() (in module PyNCBI) check_health() (PyNCBI.NCBIClient method) chromosome (PyNCBI.DbSNPRecord attribute) (PyNCBI.GeneRecord attribute) chromosome_count (PyNCBI.AssemblyRecord attribute) clear_cache() (PyNCBI.GSE method) (PyNCBI.GSM method) clear_events() (PyNCBI.ActivityReporter method) clear_response_cache() (PyNCBI.NCBIClient method) ClientMetrics (class in PyNCBI) clinical_impact (PyNCBI.ClinVarRecord attribute) clinical_significance (PyNCBI.ClinVarRecord attribute) (PyNCBI.DbSNPRecord attribute)

ClinVarRecord (class in PyNCBI) close() (PyNCBI.ByteProgressTracker method) (PyNCBI.NCBIClient method) (PyNCBI.Session method) closed (PyNCBI.Session property) column_mapping (PyNCBI.ExpressionResult attribute) columns (PyNCBI.FilePreview attribute) (PyNCBI.Table attribute) command (PyNCBI.AgentEnvelope attribute) common_name (PyNCBI.TaxonRecord attribute) complete() (PyNCBI.TaskScope method) completeness (PyNCBI.NucleotideRecord attribute) (PyNCBI.QualityReport attribute) condition_xrefs (PyNCBI.ClinVarRecord attribute) conditions (PyNCBI.ClinVarRecord attribute) confidence (PyNCBI.NormalizedValue attribute) Config (class in PyNCBI) config_scope() (in module PyNCBI) ConfigurationError configure_logging() (in module PyNCBI) conflicts (PyNCBI.HarmonizedTable attribute) ConnectionFailedError content_hash() (PyNCBI.StudyRecord method) contig_n50 (PyNCBI.AssemblyRecord attribute) coverage (PyNCBI.HarmonizedTable attribute) create_date (PyNCBI.NucleotideRecord attribute) created_at (PyNCBI.StudyBundle attribute) CRITICAL (PyNCBI.LogLevel attribute) current (PyNCBI.ActivityEvent attribute) current_bytes (PyNCBI.ByteProgressTracker property)

D

data (PyNCBI.AgentEnvelope attribute) (PyNCBI.GSM property) data_availability (PyNCBI.PMCFullText property) DATA_ON_PAGE (PyNCBI.DataStatus attribute) data_row_count (PyNCBI.GSMInfo attribute) (PyNCBI.InspectionReport attribute) (PyNCBI.SampleRecord attribute) data_status (PyNCBI.GSM property) data_type (PyNCBI.BioProjectRecord attribute) database (PyNCBI.BlastJob attribute) (PyNCBI.BlastResult attribute) DataError DataProcessingError dataset_type (PyNCBI.GEOSearchHit attribute) DataStatus (class in PyNCBI) db (PyNCBI.FASTASequence attribute) (PyNCBI.NucleotideRecord attribute) DbSNPRecord (class in PyNCBI) DEBUG (PyNCBI.LogLevel attribute) (PyNCBI.Verbosity attribute) declared_sample_count (PyNCBI.StudyRecord attribute) delete() (PyNCBI.MetadataStore method) delete_blast() (in module PyNCBI)

derive_config() (in module PyNCBI) description (PyNCBI.BioProjectRecord attribute) (PyNCBI.FASTASequence attribute) (PyNCBI.GeneRecord attribute) destination (PyNCBI.DownloadPlan attribute) division (PyNCBI.TaxonRecord attribute) doi (PyNCBI.PMCFullText attribute) (PyNCBI.PubMedArticle attribute) domain (PyNCBI.ActivityEvent attribute) done() (PyNCBI.ActivityReporter method) download_bar() (PyNCBI.ActivityReporter method) download_fastq() (in module PyNCBI) download_file() (PyNCBI.NCBIClient method) download_genome() (in module PyNCBI) download_geo_files() (in module PyNCBI) download_gse_data() (PyNCBI.GEOReader method) download_many() (in module PyNCBI) download_supplementary() (PyNCBI.GSE method) (PyNCBI.GSM method) DownloadError DownloadPlan (class in PyNCBI) downloads_folder (PyNCBI.Config attribute) dtype (PyNCBI.CharacteristicSummary attribute)

E

effective_rate_limit (PyNCBI.Config property) elapsed_ms (PyNCBI.ActivityEvent attribute) (PyNCBI.AgentEnvelope attribute) (PyNCBI.RequestEvent attribute) email (PyNCBI.Config attribute) ENA_PORTAL_API_URL (PyNCBI.Config attribute) ensure_cache_dir() (PyNCBI.Config method) entry_type (PyNCBI.GEOSearchHit attribute) ERROR (PyNCBI.LogLevel attribute) error (PyNCBI.RequestEvent attribute) error_code_for() (in module PyNCBI) error_payload() (in module PyNCBI) errors (PyNCBI.ScreeningResult attribute) esearch_ids() (in module PyNCBI) estimated_seconds (PyNCBI.BlastJob attribute) estimated_size_mb (PyNCBI.GenomeDownloadResult attribute)

esummary_docs() (in module PyNCBI) eutils_post_threshold_chars (PyNCBI.NCBIClientConfig attribute) evalue (PyNCBI.BlastHit attribute) exists (PyNCBI.NCBIFileInfo attribute) experiment_types (PyNCBI.GSEInfo attribute) (PyNCBI.InspectionReport attribute) (PyNCBI.StudyRecord attribute) export_citations() (in module PyNCBI) ExpressionResult (class in PyNCBI) extra (PyNCBI.NormalizedValue attribute) (PyNCBI.SampleRecord attribute) (PyNCBI.StudyRecord attribute) extra_headers (PyNCBI.NCBIClientConfig attribute) extra_metadata (PyNCBI.InspectionReport attribute) extract_gse_sample_info() (PyNCBI.GEOReader method) extract_gse_samples() (in module PyNCBI) extract_gsm_info() (PyNCBI.GEOReader method)

F

failed_samples (PyNCBI.GSE property) fasta_text (PyNCBI.FASTASequence attribute) FASTASequence (class in PyNCBI) fetch_assembly() (in module PyNCBI) fetch_bioprojects() (in module PyNCBI) fetch_biosamples() (in module PyNCBI) fetch_blast() (in module PyNCBI) fetch_clinvar() (in module PyNCBI) fetch_dbsnp() (in module PyNCBI) fetch_fasta() (in module PyNCBI) fetch_fastq_urls() (in module PyNCBI) fetch_genes() (in module PyNCBI) fetch_gpl_table() (in module PyNCBI) fetch_pmc_text() (in module PyNCBI) fetch_pubmed() (in module PyNCBI) fetch_sra_runs() (in module PyNCBI) fetch_taxonomy() (in module PyNCBI) fetch_variants() (in module PyNCBI) FetchMode (class in PyNCBI) field_map (PyNCBI.HarmonizedTable attribute) file_count (PyNCBI.DownloadPlan property) file_name (PyNCBI.FilePreview attribute) file_type (PyNCBI.FilePreview attribute) (PyNCBI.NCBIFileInfo attribute)

FilePreview (class in PyNCBI) files (PyNCBI.DownloadPlan attribute) (PyNCBI.GenomeDownloadResult attribute) (PyNCBI.InspectionReport attribute) (PyNCBI.StudyBundle attribute) (PyNCBI.StudyRecord attribute) filter_sections() (PyNCBI.PMCFullText method) FirstFileSelector (class in PyNCBI) fits_on_disk (PyNCBI.DownloadPlan property) format_brief() (PyNCBI.CharacteristicSummary method) format_table_preview() (in module PyNCBI) free_bytes (PyNCBI.DownloadPlan attribute) from_dict() (PyNCBI.NormalizedValue class method) (PyNCBI.QualityReport class method) (PyNCBI.SampleRecord class method) (PyNCBI.StudyRecord class method) from_string() (PyNCBI.FetchMode class method) ftp_rate_limit_per_sec (PyNCBI.Config attribute) (PyNCBI.NCBIClientConfig attribute) ftp_url (PyNCBI.GEOSearchHit attribute) full_text (PyNCBI.PubMedArticle attribute) functional_class (PyNCBI.DbSNPRecord attribute)

G

gaps (PyNCBI.BlastHit attribute) gc_percent (PyNCBI.AssemblyRecord attribute) gds_uid (PyNCBI.GEOSearchHit attribute) gene_count (PyNCBI.AssemblyRecord attribute) gene_id (PyNCBI.ClinVarRecord attribute) (PyNCBI.GeneRecord attribute) gene_ids (PyNCBI.DbSNPRecord attribute) gene_symbol (PyNCBI.ClinVarRecord attribute) gene_symbols (PyNCBI.DbSNPRecord attribute) GeneRecord (class in PyNCBI) genetic_code (PyNCBI.TaxonRecord attribute) GenomeDownloadResult (class in PyNCBI) geo_accessions (PyNCBI.PMCFullText property) geo_rate_limit_per_sec (PyNCBI.Config attribute) (PyNCBI.NCBIClientConfig attribute) GEOReader (class in PyNCBI) GEOSearchHit (class in PyNCBI) get() (PyNCBI.MetadataStore method) get_bytes() (PyNCBI.NCBIClient method) get_client() (in module PyNCBI) get_config() (in module PyNCBI) get_default_client() (in module PyNCBI) get_gds_soft_url() (PyNCBI.Config method) get_gse_info() (PyNCBI.GEOReader method) get_gsm_data_status() (PyNCBI.GEOReader method) get_json() (PyNCBI.NCBIClient method) get_logger() (in module PyNCBI) get_ncbi_batch_gsm_url() (PyNCBI.Config method)

get_ncbi_data_url() (PyNCBI.Config method) get_ncbi_query_url() (PyNCBI.Config method) get_or_build() (PyNCBI.MetadataStore method) get_range_bytes() (PyNCBI.NCBIClient method) get_reporter() (in module PyNCBI) get_series_matrix_url() (PyNCBI.Config method) get_text() (PyNCBI.NCBIClient method) grch37 (PyNCBI.ClinVarRecord attribute) grch38 (PyNCBI.ClinVarRecord attribute) GSE (class in PyNCBI) gse (PyNCBI.GSM property) gse_id (PyNCBI.ExpressionResult attribute) (PyNCBI.GSE property) (PyNCBI.GSEInfo attribute) (PyNCBI.StudyBundle attribute) (PyNCBI.StudyRecord attribute) gse_of_gsm() (in module PyNCBI) GSEInfo (class in PyNCBI) GSM (class in PyNCBI) gsm_id (PyNCBI.BioSampleRecord attribute) (PyNCBI.GSM property) (PyNCBI.GSMInfo attribute) (PyNCBI.SampleRecord attribute) gsm_ids (PyNCBI.GSEInfo attribute) (PyNCBI.InspectionReport attribute) GSMInfo (class in PyNCBI) gsms (PyNCBI.GSE property) gsms_from_gse_soft() (PyNCBI.GEOReader method)

H

harmonization (PyNCBI.StudyBundle attribute) (PyNCBI.StudyRecord attribute) harmonize_characteristics() (in module PyNCBI) harmonize_sample() (in module PyNCBI) harmonized (PyNCBI.SampleRecord attribute) harmonized_table() (PyNCBI.StudyRecord method) HarmonizedTable (class in PyNCBI) has_data (PyNCBI.GSM property) hgvs (PyNCBI.DbSNPRecord attribute) hit_count (PyNCBI.BlastResult property)

hit_frame (PyNCBI.BlastHit attribute) hit_from (PyNCBI.BlastHit attribute) hit_id (PyNCBI.BlastHit attribute) hit_num (PyNCBI.BlastHit attribute) hit_to (PyNCBI.BlastHit attribute) hits (PyNCBI.BlastResult attribute) hits_table() (PyNCBI.BlastResult method) hsp_count (PyNCBI.BlastHit attribute) http_cache_ttl (PyNCBI.Config attribute) HTTPError

I

identifiers (PyNCBI.BioSampleRecord attribute) identity (PyNCBI.BlastHit attribute) include (PyNCBI.GenomeDownloadResult attribute) index() (PyNCBI.MetadataStore method) index_name (PyNCBI.FilePreview attribute) IndexFileSelector (class in PyNCBI) info (PyNCBI.GSE property) (PyNCBI.GSM property) INFO (PyNCBI.LogLevel attribute) inspect() (PyNCBI.GEOReader method) (PyNCBI.GSE class method) (PyNCBI.GSM method) inspect_accession() (in module PyNCBI)

inspect_url() (PyNCBI.NCBIClient method) InspectionReport (class in PyNCBI) InvalidAccessionError InvalidAPIKeyError InvalidModeError is_cached() (PyNCBI.GSE method) (PyNCBI.GSM method) is_open_access (PyNCBI.PMCFullText attribute) is_ready (PyNCBI.BlastJob property) is_retryable() (in module PyNCBI) issues (PyNCBI.QualityReport attribute) items() (PyNCBI.GSE method) iter_records() (in module PyNCBI) iter_supplementary_records() (in module PyNCBI)

J

journal (PyNCBI.PMCFullText attribute) (PyNCBI.PubMedArticle attribute)

json_schema() (in module PyNCBI)

K

keys() (PyNCBI.GSE method)

keywords (PyNCBI.PubMedArticle attribute) kind (PyNCBI.PMCSection attribute)

L

last_evaluated (PyNCBI.ClinVarRecord attribute) last_modified (PyNCBI.NCBIFileInfo attribute) length (PyNCBI.BlastHit attribute) (PyNCBI.FASTASequence attribute) (PyNCBI.NucleotideRecord attribute) level (PyNCBI.PMCSection attribute) library_strategy (PyNCBI.GSMInfo attribute) (PyNCBI.SampleRecord attribute) lineage (PyNCBI.TaxonRecord attribute) lineage_ranks (PyNCBI.TaxonRecord attribute) link_accession() (in module PyNCBI) links (PyNCBI.SampleRecord attribute) (PyNCBI.StudyRecord attribute) list_gse_samples() (PyNCBI.GEOReader method) list_samples() (PyNCBI.GSE method)

load_cache() (PyNCBI.GSE method) (PyNCBI.GSM method) load_expression() (in module PyNCBI) load_gds() (in module PyNCBI) load_rnaseq_annotation() (in module PyNCBI) load_rnaseq_counts() (in module PyNCBI) (PyNCBI.GEOReader method) (PyNCBI.GSE method) load_series_matrix() (in module PyNCBI) (PyNCBI.GEOReader method) (PyNCBI.GSE method) load_study_record() (in module PyNCBI) local_downloads_folder (PyNCBI.Config property) log_level (class in PyNCBI) LogLevel (class in PyNCBI)

M

map_columns_to_gsms() (in module PyNCBI) map_location (PyNCBI.GeneRecord attribute) matrix (PyNCBI.ExpressionResult attribute) max_download_mb (PyNCBI.Config attribute) (PyNCBI.Session property) max_retries (PyNCBI.Config attribute) (PyNCBI.NCBIClientConfig attribute) message (PyNCBI.ActivityEvent attribute) (PyNCBI.BlastJob attribute) metadata (PyNCBI.ActivityEvent attribute) MetadataStore (class in PyNCBI)

method (PyNCBI.BioProjectRecord attribute) (PyNCBI.RequestEvent attribute) methods (PyNCBI.PMCFullText property) methods_available (PyNCBI.StudyBundle attribute) metrics() (PyNCBI.Session method) mito_genetic_code (PyNCBI.TaxonRecord attribute) module PyNCBI molecular_consequences (PyNCBI.ClinVarRecord attribute) molecule (PyNCBI.GSMInfo attribute) (PyNCBI.SampleRecord attribute) moltype (PyNCBI.NucleotideRecord attribute)

N

name (PyNCBI.BioProjectRecord attribute) (PyNCBI.CharacteristicSummary attribute) (PyNCBI.NCBIFileInfo attribute) NCBI_BATCH_GSM_URL_TEMPLATE (PyNCBI.Config attribute) NCBI_BLAST_URL (PyNCBI.Config attribute) NCBI_DATA_URL_TEMPLATE (PyNCBI.Config attribute) NCBI_DATASETS_BASE_URL (PyNCBI.Config attribute) NCBI_EUTILS_BASE_URL (PyNCBI.Config attribute) NCBI_FTP_HTTPS_BASE (PyNCBI.Config attribute) NCBI_GEO_DOWNLOAD_URL (PyNCBI.Config attribute) NCBI_QUERY_BASE_URL (PyNCBI.Config attribute) NCBI_QUERY_URL (PyNCBI.Config attribute) NCBI_QUERY_URL_TEMPLATE (PyNCBI.Config attribute) NCBIClient (class in PyNCBI) NCBIClientConfig (class in PyNCBI) NCBIFileInfo (class in PyNCBI)

NCBIRealmLimiter (class in PyNCBI) NetworkError next_steps (PyNCBI.AgentEnvelope attribute) NO_DATA (PyNCBI.DataStatus attribute) NoDataAvailableError non_null_count (PyNCBI.CharacteristicSummary attribute) NORMAL (PyNCBI.Verbosity attribute) normalized_table (PyNCBI.HarmonizedTable attribute) NormalizedValue (class in PyNCBI) notes (PyNCBI.DownloadPlan attribute) (PyNCBI.ExpressionResult attribute) (PyNCBI.FilePreview attribute) (PyNCBI.PMCFullText attribute) (PyNCBI.ScreeningResult attribute) NucleotideRecord (class in PyNCBI) numeric_stats (PyNCBI.CharacteristicSummary attribute)

O

ok (PyNCBI.AgentEnvelope attribute) oncogenicity (PyNCBI.ClinVarRecord attribute) operation (PyNCBI.ActivityEvent attribute) organism (PyNCBI.AssemblyRecord attribute) (PyNCBI.BioProjectRecord attribute) (PyNCBI.BioSampleRecord attribute) (PyNCBI.GeneRecord attribute) (PyNCBI.GEOSearchHit attribute) (PyNCBI.GSMInfo attribute) (PyNCBI.NucleotideRecord attribute) (PyNCBI.SampleRecord attribute)

organisms (PyNCBI.GSEInfo attribute) (PyNCBI.InspectionReport attribute) (PyNCBI.StudyRecord attribute) other_designations (PyNCBI.GeneRecord attribute) output_dir (PyNCBI.GenomeDownloadResult attribute) (PyNCBI.StudyBundle attribute) overall_design (PyNCBI.GSEInfo attribute) (PyNCBI.InspectionReport attribute) (PyNCBI.StudyRecord attribute) owner (PyNCBI.BioSampleRecord attribute)

P

package (PyNCBI.BioSampleRecord attribute) paired_accession (PyNCBI.AssemblyRecord attribute) parent_gse (PyNCBI.InspectionReport attribute) parent_taxid (PyNCBI.TaxonRecord attribute) parse_blast_xml() (in module PyNCBI) parse_characteristics() (in module PyNCBI) parse_gsm_soft() (PyNCBI.GEOReader method) ParseError path (PyNCBI.PMCSection attribute) PathTraversalError PatternFileSelector (class in PyNCBI) pause() (PyNCBI.NCBIRealmLimiter method) (PyNCBI.TokenBucketLimiter method) PER_GSM (PyNCBI.FetchMode attribute) percent_identity (PyNCBI.BlastHit property) phase (PyNCBI.ActivityEvent attribute) plan_geo_download() (in module PyNCBI) platform_id (PyNCBI.GSE property) (PyNCBI.GSEInfo attribute) (PyNCBI.GSM property) (PyNCBI.GSMInfo attribute) (PyNCBI.SampleRecord attribute) platform_of_gsm() (in module PyNCBI) platforms (PyNCBI.GEOSearchHit attribute) (PyNCBI.GSEInfo attribute) (PyNCBI.InspectionReport attribute) (PyNCBI.StudyRecord attribute) pmc_id (PyNCBI.PubMedArticle attribute) PMCFullText (class in PyNCBI) pmcid (PyNCBI.PMCFullText attribute)

PMCSection (class in PyNCBI) pmid (PyNCBI.PMCFullText attribute) (PyNCBI.PubMedArticle attribute) position_grch37 (PyNCBI.DbSNPRecord attribute) position_grch38 (PyNCBI.DbSNPRecord attribute) preview_geo_file() (in module PyNCBI) preview_rows (PyNCBI.FilePreview attribute) previous_level (PyNCBI.log_level attribute) program (PyNCBI.BlastJob attribute) (PyNCBI.BlastResult attribute) project_type (PyNCBI.BioProjectRecord attribute) protein_change (PyNCBI.ClinVarRecord attribute) (PyNCBI.DbSNPRecord attribute) protein_coding_count (PyNCBI.AssemblyRecord attribute) provenance (PyNCBI.NormalizedValue property) provenance_table (PyNCBI.HarmonizedTable attribute) provenance_table() (PyNCBI.StudyRecord method) pub_date (PyNCBI.PubMedArticle attribute) pub_year (PyNCBI.PMCFullText attribute) publication_date (PyNCBI.BioSampleRecord attribute) pubmed_ids (PyNCBI.GEOSearchHit attribute) (PyNCBI.GSEInfo attribute) (PyNCBI.InspectionReport attribute) (PyNCBI.StudyBundle attribute) (PyNCBI.StudyRecord attribute) PubMedArticle (class in PyNCBI) put() (PyNCBI.MetadataStore method) PyNCBI module pyncbi_version (PyNCBI.AgentEnvelope attribute) PyNCBIError

Q

quality (PyNCBI.StudyRecord attribute) quality_score (PyNCBI.StudyBundle attribute) QualityReport (class in PyNCBI) query (PyNCBI.ScreeningResult attribute) query_coverage (PyNCBI.BlastHit property)

query_def (PyNCBI.BlastResult attribute) query_frame (PyNCBI.BlastHit attribute) query_from (PyNCBI.BlastHit attribute) query_id (PyNCBI.BlastResult attribute) query_len (PyNCBI.BlastResult attribute) query_to (PyNCBI.BlastHit attribute)

R

rank (PyNCBI.TaxonRecord attribute) rate_limit_per_sec (PyNCBI.Config attribute) (PyNCBI.NCBIClientConfig attribute) rate_limit_stats() (PyNCBI.NCBIClient method) rate_per_sec (PyNCBI.TokenBucketLimiter property) rate_wait_ms (PyNCBI.RequestEvent attribute) RateLimitExceededError raw (PyNCBI.NormalizedValue attribute) raw_table (PyNCBI.HarmonizedTable attribute) read_supplementary_table() (in module PyNCBI) realm (PyNCBI.RequestEvent attribute) recent_events() (PyNCBI.ActivityReporter method) record() (PyNCBI.ClientMetrics method) record_cache_hit() (PyNCBI.ClientMetrics method) record_retry() (PyNCBI.ClientMetrics method) record_type (PyNCBI.InspectionReport attribute) redact_url() (in module PyNCBI) ref_allele (PyNCBI.DbSNPRecord attribute) refseq_category (PyNCBI.AssemblyRecord attribute) registration_date (PyNCBI.BioProjectRecord attribute) relations (PyNCBI.GSEInfo attribute) release_date (PyNCBI.AssemblyRecord attribute) (PyNCBI.GEOSearchHit attribute) relevance (PyNCBI.BioProjectRecord attribute) remove_gsm_cache() (PyNCBI.GSE method)

render_output() (in module PyNCBI) report (PyNCBI.StudyBundle attribute) request_count (PyNCBI.AgentEnvelope attribute) request_timeout (PyNCBI.Config attribute) RequestEvent (class in PyNCBI) RequestTimeoutError require (PyNCBI.ScreeningResult attribute) reset() (PyNCBI.ClientMetrics method) reset_config() (in module PyNCBI) resolve_cohort_files() (in module PyNCBI) resolve_pmc_id() (in module PyNCBI) retrieved_at (PyNCBI.StudyRecord attribute) retry_backoff (PyNCBI.Config attribute) (PyNCBI.NCBIClientConfig attribute) retry_statuses (PyNCBI.NCBIClientConfig attribute) review_stars (PyNCBI.ClinVarRecord attribute) review_status (PyNCBI.ClinVarRecord attribute) rid (PyNCBI.BlastJob attribute) (PyNCBI.BlastResult attribute) RNASEQ_COUNTS (PyNCBI.FetchMode attribute) rows (PyNCBI.ScreeningResult attribute) (PyNCBI.Table attribute) rsid (PyNCBI.ClinVarRecord attribute) (PyNCBI.DbSNPRecord attribute) rule (PyNCBI.NormalizedValue attribute)

S

sample_count (PyNCBI.GEOSearchHit attribute) (PyNCBI.GSE property) (PyNCBI.InspectionReport attribute) (PyNCBI.StudyBundle attribute) (PyNCBI.StudyRecord property) sample_ids_preview (PyNCBI.FilePreview attribute) sample_table (PyNCBI.ExpressionResult attribute) (PyNCBI.GSE property) sample_table() (PyNCBI.StudyRecord method) SampleRecord (class in PyNCBI) samples (PyNCBI.StudyRecord attribute) save() (PyNCBI.GSE method) (PyNCBI.GSM method) (PyNCBI.StudyRecord method) save_data() (in module PyNCBI) save_study_record() (in module PyNCBI) saved_files (PyNCBI.AgentEnvelope attribute) saved_path (PyNCBI.BlastResult attribute) (PyNCBI.ExpressionResult attribute) (PyNCBI.ScreeningResult attribute) scaffold_n50 (PyNCBI.AssemblyRecord attribute) schema_version (PyNCBI.AgentEnvelope attribute) scientific_name (PyNCBI.TaxonRecord attribute) score (PyNCBI.BlastHit attribute) (PyNCBI.QualityReport attribute) screen_studies() (in module PyNCBI) ScreeningResult (class in PyNCBI) search_assemblies() (in module PyNCBI) search_clinvar() (in module PyNCBI) search_gene() (in module PyNCBI) search_geo() (in module PyNCBI) search_ncbi() (in module PyNCBI) search_pubmed() (in module PyNCBI) search_taxonomy() (in module PyNCBI) section_filter (PyNCBI.PMCFullText attribute) sections (PyNCBI.PMCFullText attribute) select() (PyNCBI.FirstFileSelector method) (PyNCBI.IndexFileSelector method) (PyNCBI.PatternFileSelector method) (PyNCBI.SmartFileSelector method) selected_sections() (PyNCBI.PMCFullText method) sequence (PyNCBI.FASTASequence attribute) series_id (PyNCBI.GSMInfo attribute) SERIES_MATRIX (PyNCBI.FetchMode attribute) Session (class in PyNCBI) set_config() (in module PyNCBI) set_current() (PyNCBI.ByteProgressTracker method) set_level() (in module PyNCBI) set_verbosity() (PyNCBI.ActivityReporter method) shape (PyNCBI.ExpressionResult property) should_show_progress_bar() (PyNCBI.ActivityReporter method) silence() (in module PyNCBI) SILENT (PyNCBI.LogLevel attribute) (PyNCBI.Verbosity attribute) size_bytes (PyNCBI.NCBIFileInfo attribute) size_human (PyNCBI.NCBIFileInfo attribute) SmartFileSelector (class in PyNCBI) SOFTParseError source (PyNCBI.DownloadPlan attribute) (PyNCBI.ExpressionResult attribute) (PyNCBI.FilePreview attribute) (PyNCBI.NCBIFileInfo attribute) (PyNCBI.NormalizedValue attribute)

source_db (PyNCBI.AssemblyRecord attribute) (PyNCBI.NucleotideRecord attribute) source_file (PyNCBI.ExpressionResult attribute) source_key (PyNCBI.NormalizedValue attribute) source_name (PyNCBI.GSMInfo attribute) (PyNCBI.SampleRecord attribute) source_url (PyNCBI.ExpressionResult attribute) source_versions (PyNCBI.StudyRecord attribute) spdi (PyNCBI.DbSNPRecord attribute) sra_run_count (PyNCBI.StudyBundle attribute) sra_sample (PyNCBI.BioSampleRecord attribute) sra_url (PyNCBI.GSMInfo attribute) (PyNCBI.InspectionReport attribute) stats (PyNCBI.BlastResult attribute) stats() (PyNCBI.NCBIRealmLimiter method) (PyNCBI.TokenBucketLimiter method) status (PyNCBI.BlastJob attribute) status() (PyNCBI.Session method) status_code (PyNCBI.RequestEvent attribute) step() (PyNCBI.ActivityReporter method) (PyNCBI.TaskScope method) store (PyNCBI.Session property) store_cache() (PyNCBI.GSE method) (PyNCBI.GSM method) strain (PyNCBI.AssemblyRecord attribute) stream_lines() (PyNCBI.NCBIClient method) study_count (PyNCBI.ScreeningResult property) StudyBundle (class in PyNCBI) StudyRecord (class in PyNCBI) submission_count (PyNCBI.ClinVarRecord attribute) submit_blast() (in module PyNCBI) submitted_at (PyNCBI.BlastJob attribute) submitter (PyNCBI.AssemblyRecord attribute) subscribe() (PyNCBI.ActivityReporter method) subseries_bundles (PyNCBI.StudyBundle attribute) subseries_ids (PyNCBI.InspectionReport attribute) (PyNCBI.StudyRecord attribute) summarize_characteristics() (in module PyNCBI) summary (PyNCBI.AgentEnvelope attribute) (PyNCBI.GeneRecord attribute) (PyNCBI.GEOSearchHit attribute) (PyNCBI.GSEInfo attribute) (PyNCBI.InspectionReport attribute) (PyNCBI.StudyRecord attribute) summary() (PyNCBI.ClientMetrics method) (PyNCBI.HarmonizedTable method) superseries_id (PyNCBI.InspectionReport attribute) (PyNCBI.StudyRecord attribute) supp_file_types (PyNCBI.GEOSearchHit attribute) SUPPLEMENTARY (PyNCBI.FetchMode attribute) SUPPLEMENTARY_FILES (PyNCBI.DataStatus attribute) supplementary_files (PyNCBI.GSE property) (PyNCBI.GSEInfo attribute) (PyNCBI.GSM property) (PyNCBI.GSMInfo attribute) (PyNCBI.SampleRecord attribute) symbol (PyNCBI.GeneRecord attribute) SymlinkError synonyms (PyNCBI.TaxonRecord attribute)

T

Table (class in PyNCBI) table (PyNCBI.ScreeningResult property) target (PyNCBI.ActivityEvent attribute) (PyNCBI.AgentEnvelope attribute) target_material (PyNCBI.BioProjectRecord attribute) target_scope (PyNCBI.BioProjectRecord attribute) task() (PyNCBI.ActivityReporter method) TaskScope (class in PyNCBI) taxid (PyNCBI.AssemblyRecord attribute) (PyNCBI.BioProjectRecord attribute) (PyNCBI.BioSampleRecord attribute) (PyNCBI.NucleotideRecord attribute) (PyNCBI.TaxonRecord attribute) TaxonRecord (class in PyNCBI) text (PyNCBI.PMCSection attribute) text_for() (PyNCBI.PMCFullText method) there_are_hits (PyNCBI.BlastJob attribute) timeout (PyNCBI.NCBIClientConfig attribute) timestamp (PyNCBI.ActivityEvent attribute) title (PyNCBI.BioProjectRecord attribute) (PyNCBI.BioSampleRecord attribute) (PyNCBI.BlastHit attribute) (PyNCBI.ClinVarRecord attribute) (PyNCBI.GEOSearchHit attribute) (PyNCBI.GSE property) (PyNCBI.GSEInfo attribute) (PyNCBI.GSM property) (PyNCBI.GSMInfo attribute) (PyNCBI.InspectionReport attribute) (PyNCBI.NucleotideRecord attribute) (PyNCBI.PMCFullText attribute) (PyNCBI.PMCSection attribute) (PyNCBI.PubMedArticle attribute) (PyNCBI.SampleRecord attribute) (PyNCBI.StudyRecord attribute) to_bibtex() (in module PyNCBI) to_dict() (PyNCBI.ActivityEvent method) (PyNCBI.AgentEnvelope method) (PyNCBI.AssemblyRecord method) (PyNCBI.BioProjectRecord method) (PyNCBI.BioSampleRecord method) (PyNCBI.BlastHit method) (PyNCBI.BlastJob method) (PyNCBI.BlastResult method) (PyNCBI.CharacteristicSummary method) (PyNCBI.ClinVarRecord method) (PyNCBI.DbSNPRecord method) (PyNCBI.DownloadPlan method) (PyNCBI.ExpressionResult method) (PyNCBI.FASTASequence method) (PyNCBI.FilePreview method) (PyNCBI.GeneRecord method) (PyNCBI.GenomeDownloadResult method) (PyNCBI.GEOSearchHit method) (PyNCBI.GSE method) (PyNCBI.GSM method) (PyNCBI.InspectionReport method) (PyNCBI.NCBIFileInfo method) (PyNCBI.NormalizedValue method) (PyNCBI.NucleotideRecord method) (PyNCBI.PMCFullText method) (PyNCBI.PMCSection method) (PyNCBI.PubMedArticle method) (PyNCBI.QualityReport method) (PyNCBI.RequestEvent method) (PyNCBI.SampleRecord method) (PyNCBI.ScreeningResult method) (PyNCBI.Session method) (PyNCBI.StudyBundle method) (PyNCBI.StudyRecord method) (PyNCBI.TaxonRecord method)

to_json() (PyNCBI.AgentEnvelope method) to_markdown() (PyNCBI.BlastJob method) (PyNCBI.BlastResult method) (PyNCBI.DownloadPlan method) (PyNCBI.ExpressionResult method) (PyNCBI.FilePreview method) (PyNCBI.GSE method) (PyNCBI.GSM method) (PyNCBI.InspectionReport method) (PyNCBI.PMCFullText method) (PyNCBI.ScreeningResult method) (PyNCBI.StudyBundle method) (PyNCBI.StudyRecord method) to_records() (PyNCBI.GSE method) to_ris() (in module PyNCBI) to_table() (PyNCBI.GSE method) to_text() (PyNCBI.BlastJob method) (PyNCBI.BlastResult method) (PyNCBI.DownloadPlan method) (PyNCBI.ExpressionResult method) (PyNCBI.FilePreview method) (PyNCBI.InspectionReport method) (PyNCBI.PMCFullText method) (PyNCBI.ScreeningResult method) (PyNCBI.StudyBundle method) (PyNCBI.StudyRecord method) TokenBucketLimiter (class in PyNCBI) topology (PyNCBI.NucleotideRecord attribute) total (PyNCBI.ActivityEvent attribute) total_bytes (PyNCBI.DownloadPlan attribute) total_columns (PyNCBI.FilePreview attribute) total_count (PyNCBI.CharacteristicSummary attribute) total_human (PyNCBI.DownloadPlan property) total_length (PyNCBI.AssemblyRecord attribute) track() (PyNCBI.ActivityReporter method)

U

uid (PyNCBI.BioProjectRecord attribute) (PyNCBI.BioSampleRecord attribute) (PyNCBI.NucleotideRecord attribute) unique_count (PyNCBI.CharacteristicSummary attribute) unit (PyNCBI.NormalizedValue attribute) unmapped_keys (PyNCBI.HarmonizedTable attribute) update() (PyNCBI.ByteProgressTracker method) update_date (PyNCBI.NucleotideRecord attribute) update_eutils_rate() (PyNCBI.NCBIRealmLimiter method) url (PyNCBI.AssemblyRecord property) (PyNCBI.BioProjectRecord property) (PyNCBI.BioSampleRecord property) (PyNCBI.BlastJob property) (PyNCBI.ClinVarRecord property) (PyNCBI.DbSNPRecord property) (PyNCBI.FilePreview attribute) (PyNCBI.NCBIFileInfo attribute) (PyNCBI.NucleotideRecord property) (PyNCBI.RequestEvent attribute) (PyNCBI.TaxonRecord property)

V

validate_accession() (in module PyNCBI) validated (PyNCBI.DbSNPRecord attribute) value (PyNCBI.NormalizedValue attribute) value_counts (PyNCBI.CharacteristicSummary attribute) values() (PyNCBI.GSE method) variant_type (PyNCBI.ClinVarRecord attribute) variation_id (PyNCBI.ClinVarRecord attribute)

VERBOSE (PyNCBI.Verbosity attribute) verbose() (in module PyNCBI) Verbosity (class in PyNCBI) verbosity (PyNCBI.ActivityReporter property) verbosity_scope() (in module PyNCBI) verbs() (PyNCBI.Session static method) version (PyNCBI.BlastResult attribute)

W

warn() (PyNCBI.ActivityReporter method) WARNING (PyNCBI.LogLevel attribute)

warnings (PyNCBI.AgentEnvelope attribute) (PyNCBI.StudyBundle attribute)