FocalScan

[PMID: 27474725] [Nucleic Acids Research]

FocalScan: Scanning for altered genes in cancer based on coordinated DNA and RNA change

“recurrent amplifications or deletions of size-limited (focal) regions” “a tool designed to simultaneously uncover patterns of focal copy number alteration and coordinated expression change, thus combining both principles. The method outputs a ranking of tentative cancer drivers or suppressors. FocalScan works with RNA-seq data, and unlike other tools it can scan the genome unaided by a gene annotation, enabling identification of novel putatively functional elements including lncRNAs.”

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