Package index • oc2bioc

All functions
`OpenCRAVATModule-class`	mirror OpenCRAVAT module metadata to R
`OpenCRAVATModuleSet-class`	define set of R representations of OpenCRAVAT module metadata
`SO_map`	Sequence Ontology abbreviations and tags used with OpenCRAVAT
`SO_onto`	Sequence Ontology ingested from OBO
`TnTdemo()`	Illustration of variant vizualization with TnT
`as.data.frame(<OpenCRAVATModuleSet>)`	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_SO_freq()`	get the SO frequency
`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
`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 installation is encountered
`list_local_annotators()`	use reticulate/basilisk to list locally installed OpenCRAVAT annotators
`local_oc_job_resources()`	list local job folder content
`local_oc_jobids()`	list local job id folder names
`local_oc_path()`	use reticulate to determine where locally installed OpenCRAVAT modules reside
`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 a POSTable file for OpenCRAVAT
`nonco_var`	nonco_var: example output of queryOC – variant in non-coding region
`ocapp()`	simple app
`path_to_oc_executable()`	path to the primary executable
`populate_module_set()`	use reticulate to query OpenCRAVAT module store and populate an R object with metadata about available resources
`pullTF()`	utility for working with multi-experiment results from ENCODE TFBS in opencravat
`queryOC()`	single-variant query
`run_oc_req()`	build a runnable python program that posts a file of variants to OpenCRAVAT
`show(<OpenCRAVATModule>)`	display OpenCRAVAT module metadata in R
`show(<OpenCRAVATModuleSet>)`	display set of R representations of OpenCRAVAT module metadata
`var_in_tx`	var_in_tx: example output of queryOC – variant in transcribed region

Reference

All functions