Man pages for vjcitn/oc2bioc
simple interfaces from OpenCRAVAT to Bioconductor
| as.data.frame-OpenCRAVATModuleSet-method | convert some of the fields of module metadata to a data.frame |
| barplot_gene_ontology | make a gene ontology barplot over all variants |
| barplot_sequence_ontology | make a sequence ontology barplot over all variants |
| browse_oc_result | browse report from OpenCRAVAT request |
| ch19to38 | a chain object for transforming hg19 to GRCh38 coordinates |
| connect_local_annotator | connect to local annotator SQLite database |
| crx_demo | annotation of mutations in OpenCRAVAT's crx format |
| get_oc_job_status | get job status |
| get_oc_sqlite_content | get SQLite content for a table |
| get_oc_tab | get an optionally thinned table |
| get_SO_freq | get the SO frequency |
| gr38 | mutations (SNV) from TCGA ACC |
| header_tx | transform internal _header tables to char vectors |
| import_local_crx | import the 'crx' file with variant annotation |
| install_oc_module | install in the ocbenv |
| key_modules | enumerate modules that are installed by GUI when an empty... |
| list_local_annotators | use reticulate/basilisk to list locally installed OpenCRAVAT... |
| local_oc_jobids | list local job id folder names |
| local_oc_job_resources | list local job folder content |
| local_oc_path | use reticulate to determine where locally installed... |
| local_oc_sqlite_con | get connection to SQLite resource generated by a job |
| local_oc_variant_tbl | get variant tbl generated by a job |
| make_oc_POSTable | convert a GRanges to a data.frame that can be written out as... |
| nonco_var | nonco_var: example output of queryOC - variant in non-coding... |
| ocapp | simple app |
| OpenCRAVATModule-class | mirror OpenCRAVAT module metadata to R |
| OpenCRAVATModuleSet-class | define set of R representations of OpenCRAVAT module metadata |
| path_to_oc_executable | path to the primary executable |
| populate_module_set | use reticulate to query OpenCRAVAT module store and populate... |
| pullTF | utility for working with multi-experiment results from ENCODE... |
| queryOC | single-variant query |
| run_oc_req | build a runnable python program that posts a file of variants... |
| show-OpenCRAVATModule-method | display OpenCRAVAT module metadata in R |
| show-OpenCRAVATModuleSet-method | display set of R representations of OpenCRAVAT module... |
| SO_map | Sequence Ontology abbreviations and tags used with OpenCRAVAT |
| SO_onto | Sequence Ontology ingested from OBO |
| var_in_tx | var_in_tx: example output of queryOC - variant in transcribed... |
