# Bioconductor components for general cancer genomics

## Documentation for package ‘BiocOncoTK’ version 1.14.0

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

## Help Pages

add_sym | add symbols in rowData to a SummarizedExperiment that has Entrez IDs for rownames
annotTabs | table names in Annotated pancancer data release
bindMSI | bind MSI data to a SummarizedExperiment
bipg_tests | configure a bipartite graph relating tumor type to gene, using graphNEL
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.
featIDMapper | define assay-specific feature names in a character vector
fireMSI | microsatellite instability data in TCGA, collected from curatedTCGAData
get_plates | use curatedTCGAData request to acquire plate codes for samples
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
k23sig | a table of 'significant' MSIsensor-score/expression relationships in TCGA
kang_DNArepair | list of 151 genes annotated as DNA repair pathway members
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)
log10pl1 | log10(x+p) transformation for use with scales/ggplot2
map_tcga_ncit | a manually constructed table mapping TCGA acronyms to NCIT thesaurus tags
mc3toGR | create a GRanges from the MC3 mutation data
molpo_3utr | representation of 3'UTR MSI events in TCGA from Cortes-Ciriano et al. 2017
molpo_5utr | representation of 5'UTR MSI events in TCGA from Cortes-Ciriano et al. 2017
molpo_CDS | representation of MSI events in coding regions TCGA from Cortes-Ciriano et al. 2017
molpo_WGS | representation of events detected in 708 WGS experiments TCGA from Cortes-Ciriano et al. 2017
MSIsensor.10k | MSIsensor microsatellite instability scores for TCGA, collected from Ding et al. Cell 173(2) 2018.
multiviz | visualize aspects of MSIsensor/expression relationships
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
patient_to_tumor_code | data.frame mapping from TCGA patient_barcode to TCGA tumor code
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
small_msi | filtered MSI data for demonstrating exploratory app
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
viz_msi_raw | small app to survey MSIsensor against expression