Tao Wu

TL;DR: UCSCXenaShiny as discussed by the authors is an R Shiny package for quickly searching, downloading, exploring, analyzing and visualizing data from UCSC Xena data hubs, which can serve as an important complement to the current Xena genomics explorer.

TL;DR: Sigminer as mentioned in this paper is a user-friendly open-source bioinformatics tool for copy number signature extraction, analysis, and visualization, which has been applied in prostate cancer (PC), which is particularly driven by complex genome alterations.

TL;DR: Sigflow pipeline is presented, which provides an one-stop solution for de novo signature extraction, reference signature fitting, signature stability analysis, sample clustering based on signature exposure in different types of genome DNA alterations including single base substitution, doublet base substitution and deletion and copy number alteration.

TL;DR: In this paper , the authors show that the presence of ecDNA is associated with markers of tumor immune evasion, and obtaining ecDNA could be one of the mechanisms employed by tumor cells to escape immune surveillance.

TL;DR: A user-friendly open source bioinformatics tool "sigminer" has been constructed for copy number signature extraction, analysis and visualization, and copy number signatures show improved PC clinical outcome association when compared with SBS signatures.