4 packages on CRAN
A tool for implementing so called 'deft' approach (see Fisher, David J., et al. (2017) <DOI:10.1136/bmj.j573>) and model visualization.
Contains functions for identification of copy number signatures (Geoffrey et al. (2018) <doi:10.1038/s41588-018-0179-8>) and mutation signatures (Alexandrov et al. (2013) <doi:10.1038/nature12477>) by non-negative matrix factorization, signature analysis and visualization. It can be used to capture signatures of genomic variation, compare genotype or phenotype features of different signatures and thus uncover the relationship between the mechanism of genomic variation and phenotypes in cancer.
Provides a web app for downloading, analyzing and visualizing datasets from UCSC Xena, which is a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Download and explore datasets from UCSC Xena data hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded.