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 |