Man pages for seandavi/TargetOsteoAnalysis
Access Open-access TARGET Osteosarcoma Data

cosmic_censusload COSMIC gene census
extract_polyphenSplit a polyphen column into text and number
extract_siftSplit a SIFT column into text and number
get_janeway_alterationsload Janeway alterations
get_stjude_snvsget St. Jude SNVs
lcc_genesTargeted whole gene (LCC) capture gene symbols
shatterseq_resultsLoad ShatterSeq results
sleepingbeautySleeping beauty gene list from Moriarty et al.
target_cnv_callsCNV calls, corrected for purity
target_dna_qcDNA sequencing QC metrics
target_gistic_seload TARGET GISTIC data as summarized experiment
target_huex_seLoad TARGET huex data as SummarizedExperiment
target_load_clinicalload TARGET osteosarcoma data
target_methylation_seLoad TARGET methylation data as SummarizedExperiment
target_mirna_seLoad TARGET miRNA data as SummarizedExperiment
target_purityLoad Purity and Ploidy estimates
target_shiny_copy_number_survivalstart copy-number/survival shiny app
target_usi_to_samplenameconvert TARGET USI to samplename
variant_callsload stacked, filtered mutect calls
seandavi/TargetOsteoAnalysis documentation built on May 22, 2020, 8:23 p.m.