All functions

cosmic_census()

load COSMIC gene census

extract_polyphen()

Split a polyphen column into text and number

extract_sift()

Split a SIFT column into text and number

get_janeway_alterations()

load Janeway alterations

get_stjude_snvs()

get St. Jude SNVs

lcc_genes()

Targeted whole gene (LCC) capture gene symbols

shatterseq_results()

Load ShatterSeq results

sleepingbeauty

Sleeping beauty gene list from Moriarty et al.

target_cnv_calls()

CNV calls, corrected for purity

target_dna_qc()

DNA sequencing QC metrics

target_gistic_se()

load TARGET GISTIC data as summarized experiment

target_huex_se()

Load TARGET huex data as SummarizedExperiment

target_load_clinical()

load TARGET osteosarcoma data

target_methylation_se()

Load TARGET methylation data as SummarizedExperiment

target_mirna_se()

Load TARGET miRNA data as SummarizedExperiment

target_purity()

Load Purity and Ploidy estimates

target_shiny_copy_number_survival()

start copy-number/survival shiny app

target_usi_to_samplename()

convert TARGET USI to samplename

variant_calls()

load stacked, filtered mutect calls