Man pages for bahlolab/cavalier
Assist With Variant Interpretation Phase Of Next Generation Sequencing Analysis Pipeline
| build_caches | Build local disk caches |
| build_disease_name_cache | Build a complete cache of disease names |
| build_panelapp_cache | Store local cache of all PanelApp panels |
| cache | Save or load disk cache |
| cache_file | Store or load extenal file to disk |
| cavalier | cavalier: Candidate Variant List Evaluation Report |
| clear_memory_caches | Removes memory cache for functions memoised with... |
| ensembl2gevir | Convert ensemble gene id to GeVIR percentile |
| ensembl2loeuf | Convert ensemble gene id to to (ExAC) LOUEF percentile |
| get_centromeres_gaps | Get assembly gap and centromere locations for... |
| get_disease_name_cache | Get latest disease name cache from disk |
| get_disease_names | Convert HPO disease_id to disease name |
| get_g4e_full_list | Retrieve Genes4Epilepsy from GitHub |
| get_g4e_phenotype_list | Get sublist of Genes4Epilepsy by phenotype |
| get_g4e_version | Get HPO version from GitHub or disk cache |
| get_gene_disease_map | Simplified mapping from gene to phenotype from HPO |
| get_gene_list | Return a gene list from PanelApp, HPO or Genes4Epilepsy |
| get_genes_to_phenotype | HPO genes_to_phenotype table |
| get_gevir_table | Retrieve GeVIR table from get_cavalier_opt("gevir_url") or... |
| get_gevir_table_hgnc | Update GeVIR table gene symbol with current HGNC symbol |
| get_gtex_expression_hgnc | Replace symbol in GTEx expression with current HGNC version |
| get_hgnc_alias | Get HGNC gene symbols alias table to convert symbols to... |
| get_hgnc_complete | Get HGNC complete table from either... |
| get_hgnc_ensembl | Get HGNC hgnc_id, ensemble_gene_id table |
| get_hgnc_entrez | Get HGNC hgnc_id, entrez_id table |
| get_hgnc_locus_group | Get HGNC hgnc_id, locus_group table |
| get_hgnc_locus_group_list | Get list of from HGNC by locus_group |
| get_hgnc_symbol | Get HGNC hgnc_id, symbol table |
| get_hgnc_version | Get HGNC version from either... |
| get_hpo_g2p_p2g | Retrieve HPO genes_to_phenotype and phenotype_to_genes |
| get_hpo_gene_list | Get a gene list from HPO phenotype_to_genes table |
| get_hpo_term_names | Mapping of hpo_term_id to hpo_term_name |
| get_hpo_version | Get HPO version from GitHub or disk cache |
| get_panelapp_panel | Get gene panel from PanelApp API |
| get_panelapp_panels | Get table of all current PanelApp panels |
| get_panelapp_panel_version | Get latest version of PanelApp Panel (from server or cache) |
| get_panelapp_url | Get URL for PanelApp API |
| get_panelapp_version_history | Get version history for PanelApp panel |
| get_phenotype_to_genes | HPO phenotype_to_genes table |
| get_version | Get the latest version from online on cache depending on... |
| hgnc_ensembl2entrez | Convert ensembl_gene_id to entrez_id |
| hgnc_ensembl2id | Convert ensembl_gene_id to hgnc_id |
| hgnc_ensembl2sym | Convert ensembl_gene_id to symbol |
| hgnc_entrez2ensembl | Convert entrez_id to ensembl_gene_id |
| hgnc_entrez2id | Convert entrez_id to hgnc_id |
| hgnc_entrez2sym | Convert entrez_id to symbol |
| hgnc_id2ensembl | Convert hgnc_id to ensembl_gene_id |
| hgnc_id2entrez | Convert hgnc_id to entrez_id |
| hgnc_id2sym | Convert hgnc_id to symbol |
| hgnc_sym2ensembl | Convert symbol to ensembl_gene_id |
| hgnc_sym2entrez | Convert symbol to entrez_id |
| hgnc_sym2id | Convert gene symbol to hgnc_id |
| hpo_api_get | Query HPO API |
| hpo_api_get_disease_names | Query HPO API for disease name with disease id |
| hpo_api_get_diseases_by_gene | Query HPO API for diseases associates with gene, returning... |
| hpo_id2name | convert hpo_term_id to hpo_term_name |
| hpo_mendelian_inheritnace | Mendelian inheritance terms for assigning inheritance to HPO... |
| plot_gtex_expression | Plot GTEx tissue median RPKM expression for given gene symbol |
| sym2gevir | Convert HGNC gene symbol to GeVIR percentile |
| sym2loeuf | Convert HGNC gene symbol to (ExAC) LOUEF percentile |
