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