rnalysis.filtering.DESeqFilter.find_paralogs_pantherļƒ

DESeqFilter.find_paralogs_panther(organism: Literal['auto'] | str | int | Literal = 'auto', gene_id_type: str | Literal['auto'] | Literal['UniProtKB AC/ID', 'UniParc', 'UniRef50', 'UniRef90', 'UniRef100', 'Gene Name', 'CRC64', 'Proteome ID', 'Ensembl', 'Ensembl Genomes', 'Ensembl Genomes Protein', 'Ensembl Genomes Transcript', 'Ensembl Protein', 'Ensembl Transcript', 'GeneID', 'KEGG', 'PATRIC', 'UCSC', 'WBParaSite', 'WBParaSite Transcript/Protein', 'ArachnoServer', 'Araport', 'CGD', 'ClinPGx', 'ConoServer', 'dictyBase', 'EchoBASE', 'euHCVdb', 'FlyBase', 'GeneCards', 'GeneReviews', 'HGNC', 'LegioList', 'Leproma', 'MaizeGDB', 'MGI', 'MIM', 'OpenTargets', 'Orphanet', 'PomBase', 'PseudoCAP', 'RGD', 'SGD', 'TubercuList', 'VEuPathDB', 'VGNC', 'WormBase', 'WormBase Protein', 'WormBase Transcript', 'Xenbase', 'ZFIN', 'eggNOG', 'GeneTree', 'HOGENOM', 'OMA', 'OrthoDB', 'CCDS', 'EMBL/GenBank/DDBJ', 'EMBL/GenBank/DDBJ CDS', 'GI number', 'PIR', 'RefSeq Nucleotide', 'RefSeq Protein', 'ChiTaRS', 'GeneWiki', 'GenomeRNAi', 'PHI-base', 'CollecTF', 'BioCyc', 'PlantReactome', 'Reactome', 'UniPathway', 'CPTAC', 'ProteomicsDB'] = 'auto')ļƒ

Find paralogs within the same species using the PantherDB database.

Parameters:

  • organism (str or int) ā€“ organism name or NCBI taxon ID of the input genesā€™ source species.

  • gene_id_type (str or 'auto' (default='auto')) ā€“ the identifier type of the genes/features in the FeatureSet object (for example: ā€˜UniProtKBā€™, ā€˜WormBaseā€™, ā€˜RNACentralā€™, ā€˜Entrez Gene IDā€™). If the annotations fetched from the KEGG server do not match your gene_id_type, RNAlysis will attempt to map the annotationsā€™ gene IDs to your identifier type. For a full list of legal ā€˜gene_id_typeā€™ names, see the UniProt website: https://www.uniprot.org/help/api_idmapping

Returns:

DataFrame describing all discovered paralog mappings.