Man pages for bahlolab/cavalier
Assist With Variant Interpretation Phase Of Next Generation Sequencing Analysis Pipeline

build_cachesBuild local disk caches
build_disease_name_cacheBuild a complete cache of disease names
build_panelapp_cacheStore local cache of all PanelApp panels
cacheSave or load disk cache
cache_fileStore or load extenal file to disk
cavaliercavalier: Candidate Variant List Evaluation Report
clear_memory_cachesRemoves memory cache for functions memoised with...
ensembl2gevirConvert ensemble gene id to GeVIR percentile
ensembl2loeufConvert ensemble gene id to to (ExAC) LOUEF percentile
get_centromeres_gapsGet assembly gap and centromere locations for...
get_disease_name_cacheGet latest disease name cache from disk
get_disease_namesConvert HPO disease_id to disease name
get_g4e_full_listRetrieve Genes4Epilepsy from GitHub
get_g4e_phenotype_listGet sublist of Genes4Epilepsy by phenotype
get_g4e_versionGet HPO version from GitHub or disk cache
get_gene_disease_mapSimplified mapping from gene to phenotype from HPO
get_gene_listReturn a gene list from PanelApp, HPO or Genes4Epilepsy
get_genes_to_phenotypeHPO genes_to_phenotype table
get_gevir_tableRetrieve GeVIR table from get_cavalier_opt("gevir_url") or...
get_gevir_table_hgncUpdate GeVIR table gene symbol with current HGNC symbol
get_gtex_expression_hgncReplace symbol in GTEx expression with current HGNC version
get_hgnc_aliasGet HGNC gene symbols alias table to convert symbols to...
get_hgnc_completeGet HGNC complete table from either...
get_hgnc_ensemblGet HGNC hgnc_id, ensemble_gene_id table
get_hgnc_entrezGet HGNC hgnc_id, entrez_id table
get_hgnc_locus_groupGet HGNC hgnc_id, locus_group table
get_hgnc_locus_group_listGet list of from HGNC by locus_group
get_hgnc_symbolGet HGNC hgnc_id, symbol table
get_hgnc_versionGet HGNC version from either...
get_hpo_g2p_p2gRetrieve HPO genes_to_phenotype and phenotype_to_genes
get_hpo_gene_listGet a gene list from HPO phenotype_to_genes table
get_hpo_term_namesMapping of hpo_term_id to hpo_term_name
get_hpo_versionGet HPO version from GitHub or disk cache
get_panelapp_panelGet gene panel from PanelApp API
get_panelapp_panelsGet table of all current PanelApp panels
get_panelapp_panel_versionGet latest version of PanelApp Panel (from server or cache)
get_panelapp_urlGet URL for PanelApp API
get_panelapp_version_historyGet version history for PanelApp panel
get_phenotype_to_genesHPO phenotype_to_genes table
get_versionGet the latest version from online on cache depending on...
hgnc_ensembl2entrezConvert ensembl_gene_id to entrez_id
hgnc_ensembl2idConvert ensembl_gene_id to hgnc_id
hgnc_ensembl2symConvert ensembl_gene_id to symbol
hgnc_entrez2ensemblConvert entrez_id to ensembl_gene_id
hgnc_entrez2idConvert entrez_id to hgnc_id
hgnc_entrez2symConvert entrez_id to symbol
hgnc_id2ensemblConvert hgnc_id to ensembl_gene_id
hgnc_id2entrezConvert hgnc_id to entrez_id
hgnc_id2symConvert hgnc_id to symbol
hgnc_sym2ensemblConvert symbol to ensembl_gene_id
hgnc_sym2entrezConvert symbol to entrez_id
hgnc_sym2idConvert gene symbol to hgnc_id
hpo_api_getQuery HPO API
hpo_api_get_disease_namesQuery HPO API for disease name with disease id
hpo_api_get_diseases_by_geneQuery HPO API for diseases associates with gene, returning...
hpo_id2nameconvert hpo_term_id to hpo_term_name
hpo_mendelian_inheritnaceMendelian inheritance terms for assigning inheritance to HPO...
plot_gtex_expressionPlot GTEx tissue median RPKM expression for given gene symbol
sym2gevirConvert HGNC gene symbol to GeVIR percentile
sym2loeufConvert HGNC gene symbol to (ExAC) LOUEF percentile
bahlolab/cavalier documentation built on June 30, 2024, 8:35 a.m.