Man pages for vjcitn/BiocOncoTK
Bioconductor components for general cancer genomics

add_symadd symbols in rowData to a SummarizedExperiment that has...
annotTabstable names in Annotated pancancer data release
bindMSIbind MSI data to a SummarizedExperiment
bipg_testsconfigure a bipartite graph relating tumor type to gene,...
brcaMAEa virtual MultiAssayExperiment for pancancer-atlas BRCA data
buildPancanSEhelper for SummarizedExperiment construction from pancan
CCLE_DRUG_BROADCCLE_DRUG_BROAD: serialization of legacy CCLE 'Drug data'...
cell_70138cell_70138: a table with cell-line information from LINCS
clueDemosgenerate lists to generate clue API queries
clueServiceNamesProvide names of some clue.io services for which examples are...
darmGBMclsData in count_lstpm format from Darmanis 2017 (PMC 5810554)...
dingMSImicrosatellite instability data in TCGA, collected from Ding...
featIDMapperdefine assay-specific feature names in a character vector
fireMSImicrosatellite instability data in TCGA, collected from...
get_platesuse curatedTCGAData request to acquire plate codes for...
ggFeatDenscreate ggplot for density of starts of a GRanges in an...
ggFeatureSegsgenerate a ggplot of segments of gene-like regions
ggMutDensmake a ggplot with density traces of mutations per base pair,...
icd10_chelper for interpreting ICD-10 codes
k23siga table of 'significant' MSIsensor-score/expression...
kang_DNArepairlist of 151 genes annotated as DNA repair pathway members
loadPateluse BiocFileCache discipline to acquire patelGBMSC...
log10pl1log10(x+p) transformation for use with scales/ggplot2
map_tcga_ncita manually constructed table mapping TCGA acronyms to NCIT...
mc3toGRcreate a GRanges from the MC3 mutation data
molpo_3utrrepresentation of 3'UTR MSI events in TCGA from...
molpo_5utrrepresentation of 5'UTR MSI events in TCGA from...
molpo_CDSrepresentation of MSI events in coding regions TCGA from...
molpo_WGSrepresentation of events detected in 708 WGS experiments TCGA...
MSIsensor.10kMSIsensor microsatellite instability scores for TCGA,...
multivizvisualize aspects of MSIsensor/expression relationships
oncoPrintISBinteractive interface to ComplexHeatmap oncoPrint with inputs...
pancan_appprovide a shiny app to 'glimpse' structure and content of...
pancan_BQprovide bigrquery connection to pancancer Annotated datasets
pancan_clinicalTabVarnamesgive an interface to tablenames
pancan.clin.varnamespancan.clin.varnames: a data.frame with a list of variable...
pancan_longnameutility to help find long table names
pancan_sampTypeMaphelper for interpreting pancan-atlas sample type codes
pancan_tabulatetabulate a variable in a table
patient_to_tumor_codedata.frame mapping from TCGA patient_barcode to TCGA tumor...
pert_70138pert_70138: a table with perturbagen information from LINCS
pertClassesenumerate perturbagen classes
query_cluerun the api.clue.io API to acquire information on LINCS...
reexportsObjects exported from other packages
replaceRownamesmap rownames of an SE to another vocabulary
small_msifiltered MSI data for demonstrating exploratory app
TcgaMutCountsobtain data frame with counts of mutation per gene symbol for...
TcgaNIndWithAnyMutGive count of individuals with a mutation recorded for...
tumNorSetcreate list with SEs for tumor and normal for a tumor/assay...
utilsutilities for mock data (not involving internet access for...
viz_msi_rawsmall app to survey MSIsensor against expression
vjcitn/BiocOncoTK documentation built on Feb. 14, 2023, 11:56 p.m.