Datasets
TCGA Tumorscape: Our copy-number analyses of almost 11,000 TCGA cancers
Tumorscape: Copy-number analyses of 3131 cancers from Beroukhim et al, Nature 2010
Our data in the Gene Expression Omnibus
Tools
GISTIC 2.0 for analysis of recurrent copy-number alterations
SvABA for rearrangements detection by local assembly
Tangent for copy-number normalization
VariantBam for BAM filtering and profiling
SeqLib for interrogating sequencing data
SVlib for benchmarking variant callers
ASCETS for quantifying aneuploidy
GISTIC 1.0 for analysis of recurrent copy-number alterations