Method List
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GRC_build Organism
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_get_file Ensembl::FTP
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_get_gz Ensembl::FTP
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#abstract PubMed::Article
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#add BibTexFile
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#aka Entrez::Gene
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align Cath
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allowed_biomart_archives Organism
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ancestors_in GO
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attach_translations Organism
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#author PubMed::Article
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base_url Ensembl::FTP
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#bibentry PubMed::Article
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#bibtex PubMed::Article
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cath UniProt
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cath_domains UniProt
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cath_index Cath
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chromosome EBChromatin
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chromosome_sizes Organism
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citation_link GoogleScholar
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clean_string BibTexFile
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cohort_dataset Xena
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cohorts Xena
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#comentaries Entrez::Gene
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compare_archives Organism
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create_directories Synapse
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create_directory Synapse
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default_code Organism
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descendants GO
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#description Entrez::Gene
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description KEGG
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descriptions KEGG
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directory_structure Synapse
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domain_sequences Cath
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domains_for_pdb Cath
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ensembl_tsv Ensembl::FTP
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entrez2name Entrez
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entrez2native Entrez
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entrez2pubmed Entrez
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entrez_taxid_organism Organism
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#entries BibTexFile
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#entry BibTexFile
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escape_title PubMed::Article
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features UniProt
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#fields BibTexFile::Entry
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fields_for Ensembl::FTP
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filter NCIBioCartaPathway
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filter NCIReactomePathway
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filter NCINaturePathway
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filter ReactomePathway
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filter KeggPathway
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ftp_name_for Ensembl::FTP
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ftp_name_for_domain Ensembl::FTP
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ftp_url_for Ensembl::FTP
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#full_text PubMed::Article
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full_text_url GoogleScholar
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gene_index NCIBioCartaPathway
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gene_index ReactomePathway
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gene_index NCINaturePathway
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gene_index NCIReactomePathway
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gene_list_bases Organism
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gene_list_exon_bases Organism
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get_article PubMed
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get_organism_ids UniProt
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get_uniprot_entry UniProt
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get_uniprot_sequence UniProt
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goterms GO
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group_genes GO
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#gscholar_pdf PubMed::Article
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guess_id Organism
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has_table? Ensembl::FTP
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hg_build Organism
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id2ancestors GO
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id2name KEGG
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id2name GO
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id2namespace GO
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index2ens KEGG
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index2genes KEGG
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index2kegg KEGG
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#info BibTexFile::Entry
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info GO
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init GO
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#initialize BibTexFile
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#initialize BibTexFile::Entry
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#initialize PubMed::Article
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#initialize Entrez::Gene
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installable_organisms Organism
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installed_organisms Organism
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#journal PubMed::Article
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known_ids Organism
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liftOver Organism
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load_file BibTexFile
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make_bibentry PubMed::Article
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make_organism Organism
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#mesh PubMed::Article
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#method_missing BibTexFile::Entry
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#name BibTexFile::Entry
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name Pfam
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name2id KEGG
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name_index ReactomePathway
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name_index Pfam
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name_index NCIBioCartaPathway
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name_index NCINaturePathway
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name_index NCIReactomePathway
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names KEGG
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normalize Organism
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number_cites GoogleScholar
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oncogenes OncoDriveROLE
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org2release Ensembl
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organism Oreganno
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organism Signor
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organism PhosphoELM
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#organism Entrez::Gene
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organism Organism
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organism OncoDriveROLE
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organism MSigDB
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organism CORUM
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organism MCLP
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organism GTRD
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organism PRO
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organism CancerGenomeInterpreter
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organism PhosphoSitePlus
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organism Reactome
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organism_code Organism
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organism_codes Organism
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organism_for_build Organism
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organism_hg19 ClinVar
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organism_hg38 ClinVar
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organisms Organism
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parse_bibtex BibTexFile
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parse_entry BibTexFile
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parse_xml PubMed::Article
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pdb_index Cath
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pdbs Cath
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pdbs UniProt
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pdbs_covering_aa_position UniProt
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#pdf_url PubMed::Article
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pfam_index InterPro
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#pmc_full_xml PubMed::Article
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#pmc_pdf PubMed::Article
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#pmid PubMed::Article
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prepared_organisms Organism
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process_interactions CASCADE
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process_members CASCADE
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process_paradigm CASCADE
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#protnames Entrez::Gene
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python_create_dir Synapse
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python_file_template Synapse
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python_login Synapse
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python_upload_template Synapse
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query BioMart
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query PubMed
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query Xena
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rake_organism_helper Organism
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releases Ensembl
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#save BibTexFile
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scientific_name Organism
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sequence UniProt
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#substance PubMed::Article
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#summary Entrez::Gene
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#symbol Entrez::Gene
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#text PubMed::Article
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#text Entrez::Gene
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#title PubMed::Article
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#to_s BibTexFile::Entry
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tpm ArrayExpress
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tsv BioMart
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tsv Xena
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#type BibTexFile::Entry
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unclassified Cath
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upload_dir Synapse
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upload_file Synapse
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upload_files Synapse
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url_for Ensembl::FTP
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user_agent GoogleScholar
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variants UniProt