# Bioconductor components for general cancer genomics

## Documentation for package ‘BiocOncoTK’ version 1.2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

annotTabs | table names in Annotated pancancer data release
bindMSI | bind MSI data to a SummarizedExperiment
brcaMAE | a virtual MultiAssayExperiment for pancancer-atlas BRCA data
buildPancanSE | helper for SummarizedExperiment construction from pancan
CCLE_DRUG_BROAD | CCLE_DRUG_BROAD: serialization of legacy CCLE 'Drug data' from Broad Institute
cell_70138 | cell_70138: a table with cell-line information from LINCS
clueDemos | generate lists to generate clue API queries
clueServiceNames | Provide names of some clue.io services for which examples are available in this package.
darmGBMcls | Data in count_lstpm format from Darmanis 2017 (PMC 5810554) single cell RNA-seq in GBM
dingMSI | microsatellite instability data in TCGA, collected from Ding et al. Cell 173(2) 2018.
fireMSI | microsatellite instability data in TCGA, collected from curatedTCGAData
ggFeatDens | create ggplot for density of starts of a GRanges in an interval
ggFeatureSegs | generate a ggplot of segments of gene-like regions
ggMutDens | make a ggplot with density traces of mutations per base pair, for 'most mutated' tumor types in a given interval
icd10_c | helper for interpreting ICD-10 codes
loadPatel | use BiocFileCache discipline to acquire patelGBMSC SummarizedExperiment
load_ccleNRAS | utilities for mock data (not involving internet access for vignette)
load_nrasdf | utilities for mock data (not involving internet access for vignette)
load_NRAS_AHR | utilities for mock data (not involving internet access for vignette)
mc3toGR | create a GRanges from the MC3 mutation data
oncoPrintISB | interactive interface to ComplexHeatmap oncoPrint with inputs from ISB Cancer Genomics Cloud BigQuery back end
pancan.clin.varnames | pancan.clin.varnames: a data.frame with a list of variable names for clinical patient data
pancan_app | provide a shiny app to 'glimpse' structure and content of pancan atlas
pancan_BQ | provide bigrquery connection to pancancer Annotated datasets
pancan_clinicalTabVarnames | give an interface to tablenames
pancan_longname | utility to help find long table names
pancan_sampTypeMap | helper for interpreting pancan-atlas sample type codes
pancan_tabulate | tabulate a variable in a table
pertClasses | enumerate perturbagen classes
pert_70138 | pert_70138: a table with perturbagen information from LINCS
query_clue | run the api.clue.io API to acquire information on LINCS experiments
replaceRownames | map rownames of an SE to another vocabulary
TcgaMutCounts | obtain data frame with counts of mutation per gene symbol for selected tumor type
TcgaNIndWithAnyMut | Give count of individuals with a mutation recorded for selected tumor
tumNorSet | create list with SEs for tumor and normal for a tumor/assay pairing