Man pages for vjcitn/oc2bioc
simple interfaces from OpenCRAVAT to Bioconductor

as.data.frame-OpenCRAVATModuleSet-methodconvert some of the fields of module metadata to a data.frame
barplot_gene_ontologymake a gene ontology barplot over all variants
barplot_sequence_ontologymake a sequence ontology barplot over all variants
browse_oc_resultbrowse report from OpenCRAVAT request
ch19to38a chain object for transforming hg19 to GRCh38 coordinates
connect_local_annotatorconnect to local annotator SQLite database
crx_demoannotation of mutations in OpenCRAVAT's crx format
get_oc_job_statusget job status
get_oc_sqlite_contentget SQLite content for a table
get_oc_tabget an optionally thinned table
get_SO_freqget the SO frequency
gr38mutations (SNV) from TCGA ACC
header_txtransform internal _header tables to char vectors
import_local_crximport the 'crx' file with variant annotation
install_oc_moduleinstall in the ocbenv
key_modulesenumerate modules that are installed by GUI when an empty...
list_local_annotatorsuse reticulate/basilisk to list locally installed OpenCRAVAT...
local_oc_jobidslist local job id folder names
local_oc_job_resourceslist local job folder content
local_oc_pathuse reticulate to determine where locally installed...
local_oc_sqlite_conget connection to SQLite resource generated by a job
local_oc_variant_tblget variant tbl generated by a job
make_oc_POSTableconvert a GRanges to a data.frame that can be written out as...
nonco_varnonco_var: example output of queryOC - variant in non-coding...
ocappsimple app
OpenCRAVATModule-classmirror OpenCRAVAT module metadata to R
OpenCRAVATModuleSet-classdefine set of R representations of OpenCRAVAT module metadata
path_to_oc_executablepath to the primary executable
populate_module_setuse reticulate to query OpenCRAVAT module store and populate...
pullTFutility for working with multi-experiment results from ENCODE...
queryOCsingle-variant query
run_oc_reqbuild a runnable python program that posts a file of variants...
show-OpenCRAVATModule-methoddisplay OpenCRAVAT module metadata in R
show-OpenCRAVATModuleSet-methoddisplay set of R representations of OpenCRAVAT module...
SO_mapSequence Ontology abbreviations and tags used with OpenCRAVAT
SO_ontoSequence Ontology ingested from OBO
var_in_txvar_in_tx: example output of queryOC - variant in transcribed...
vjcitn/oc2bioc documentation built on Jan. 31, 2021, 6:20 p.m.