Bioconductor components for general cancer genomics

Documentation for package ‘BiocOncoTK’ version 1.22.0

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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
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