CCLE_DRUG_BROAD         CCLE_DRUG_BROAD: serialization of legacy CCLE
                        'Drug data' from Broad Institute
MSIsensor.10k           MSIsensor microsatellite instability scores for
                        TCGA, collected from Ding et al. Cell 173(2)
                        2018.
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
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
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)
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
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_BQ               provide bigrquery connection to pancancer
                        Annotated datasets
pancan_app              provide a shiny app to 'glimpse' structure and
                        content of pancan atlas
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
tumNorSet               create list with SEs for tumor and normal for a
                        tumor/assay pairing
viz_msi_raw             small app to survey MSIsensor against
                        expression
