Index A | B | C | D | E | F | G | I | L | M | O | P | Q | R | S | T | U | V | X A apply_dataframe_enrichment() (in module pysradb.metadata_enrichment) ArgParser (class in pysradb.cli) B bioproject_to_srp() (pysradb.sraweb.SRAweb method) C confirm() (in module pysradb.utils) copyfileobj() (in module pysradb.utils) create_esummary_params() (pysradb.sraweb.SRAweb method) create_metadata_extractor() (in module pysradb.metadata_enrichment) CustomFormatterArgP (class in pysradb.cli) D doi_to_gse() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) doi_to_identifiers() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) doi_to_pmid() (pysradb.sraweb.SRAweb method) doi_to_srp() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) download() (in module pysradb.cli) (pysradb.geoweb.GEOweb method) download_file() (in module pysradb.download) download_geo_matrix() (in module pysradb.geoweb) E EmbeddingMetadataExtractor (class in pysradb.metadata_enrichment) EnaSearch (class in pysradb.search) enrich_dataframe() (pysradb.metadata_enrichment.MetadataExtractor method) error() (pysradb.cli.ArgParser method) expand_sample_attribute_columns() (in module pysradb.filter_attrs) extract_batch() (pysradb.metadata_enrichment.MetadataExtractor method) extract_external_sources() (pysradb.sraweb.SRAweb method) extract_identifiers_from_text() (pysradb.sraweb.SRAweb method) extract_metadata() (pysradb.metadata_enrichment.EmbeddingMetadataExtractor method) (pysradb.metadata_enrichment.LLMMetadataExtractor method) (pysradb.metadata_enrichment.MetadataExtractor method) F fetch_bioproject_pmids() (pysradb.sraweb.SRAweb method) fetch_ena_fastq() (pysradb.sraweb.SRAweb method) fetch_gds_results() (pysradb.sraweb.SRAweb method) fetch_gsm_soft() (pysradb.sraweb.SRAweb method) fetch_pmc_fulltext() (pysradb.sraweb.SRAweb method) format_xml() (pysradb.sraweb.SRAweb static method) G geo_matrix() (in module pysradb.cli) geo_metadata() (pysradb.sraweb.SRAweb method) GeoSearch (class in pysradb.search) GEOweb (class in pysradb.geoweb) get_df() (pysradb.search.QuerySearch method) get_download_links() (pysradb.geoweb.GEOweb method) get_efetch_response() (pysradb.sraweb.SRAweb method) get_esummary_response() (pysradb.sraweb.SRAweb method) get_file_size() (in module pysradb.download) get_geo_search_info() (in module pysradb.cli) get_gzip_uncompressed_size() (in module pysradb.utils) get_plot_objects() (pysradb.search.QuerySearch method) get_retmax() (in module pysradb.sraweb) get_uids() (pysradb.search.SraSearch method) gse_to_gsm() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) gse_to_pmid() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) gse_to_srp() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) gsm_to_gse() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) gsm_to_srp() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) gsm_to_srr() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) gsm_to_srs() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) gsm_to_srx() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) guess_cell_type() (in module pysradb.filter_attrs) guess_strain_type() (in module pysradb.filter_attrs) guess_tissue_type() (in module pysradb.filter_attrs) I IncorrectFieldException info() (pysradb.search.GeoSearch class method) L LLMMetadataExtractor (class in pysradb.metadata_enrichment) load_ontology_reference() (in module pysradb.metadata_enrichment) M md5_validate_file() (in module pysradb.download) metadata() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) MetadataExtractor (class in pysradb.metadata_enrichment) millify() (in module pysradb.download) MissingQueryException mkdir_p() (in module pysradb.utils) module pysradb pysradb.cli pysradb.download pysradb.exceptions pysradb.filter_attrs pysradb.geoweb pysradb.metadata_enrichment pysradb.search pysradb.sraweb pysradb.taxid2name pysradb.utils O order_dataframe() (in module pysradb.utils) P parse_args() (in module pysradb.cli) parse_geo_matrix_to_tsv() (in module pysradb.geoweb) path_leaf() (in module pysradb.utils) pmc_to_identifiers() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) pmid_to_gse() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) pmid_to_identifiers() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) pmid_to_pmc() (pysradb.sraweb.SRAweb method) pmid_to_srp() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) pretty_print_df() (in module pysradb.cli) pysradb module pysradb.cli module pysradb.download module pysradb.exceptions module pysradb.filter_attrs module pysradb.geoweb module pysradb.metadata_enrichment module pysradb.search module pysradb.sraweb module pysradb.taxid2name module pysradb.utils module Q QuerySearch (class in pysradb.search) R requests_3_retries() (in module pysradb.utils) run_command() (in module pysradb.utils) S scientific_name_to_taxid() (in module pysradb.utils) search() (in module pysradb.cli) (pysradb.search.EnaSearch method) (pysradb.search.GeoSearch method) (pysradb.search.QuerySearch method) (pysradb.search.SraSearch method) (pysradb.sraweb.SRAweb method) search_pmc_for_external_sources() (pysradb.sraweb.SRAweb method) show_result_statistics() (pysradb.search.QuerySearch method) sra_metadata() (pysradb.sraweb.SRAweb method) sra_to_pmid() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) SraSearch (class in pysradb.search) SRAweb (class in pysradb.sraweb) srp_to_gse() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) srp_to_pmid() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) srp_to_srr() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) srp_to_srs() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) srp_to_srx() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) srr_to_gsm() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) srr_to_pmid() (pysradb.sraweb.SRAweb method) srr_to_srp() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) srr_to_srs() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) srr_to_srx() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) srs_to_gsm() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) srs_to_pmid() (pysradb.sraweb.SRAweb method) srs_to_srx() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) srx_to_gsm() (pysradb.sraweb.SRAweb method) srx_to_pmid() (pysradb.sraweb.SRAweb method) srx_to_srp() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) srx_to_srr() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) srx_to_srs() (in module pysradb.cli) (pysradb.sraweb.SRAweb method) T TqdmUpTo (class in pysradb.utils) U unique() (in module pysradb.utils) update_to() (pysradb.utils.TqdmUpTo method) V visualise_results() (pysradb.search.QuerySearch method) X xml_to_json() (pysradb.sraweb.SRAweb static method) xmlescape() (in module pysradb.sraweb)