Bioconductor components for general cancer genomics


[Up] [Top]

Documentation for package ‘BiocOncoTK’ version 1.2.1

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