![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
| 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 |
| 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 |