Name: Daniele Ramazzotti
Type: User
Company: University of Milano-Bicocca, Milano, Italy
Bio: Department of Medicine and Surgery, University of Milano-Bicocca, Milano, Italy
Twitter: ramazzottidani
Location: Milano, Italy
Blog: https://sites.google.com/site/danieleramazzotti1/
Daniele Ramazzotti's Projects
ASCETIC (Agony-baSed Cancer EvoluTion InferenCe) is a novel framework for the inference of a set of statistically significant temporal patterns involving alternations in driver genes from cancer genomics data. Manuscript published at: https://www.nature.com/articles/s41467-023-41670-3
Mutational signature analysis for the BRCA project.
Implementations in both Matlab and R of the CIMLR method. The manuscript of the method is available at: https://www.nature.com/articles/s41467-018-06921-8
This repository provides all the code to replicate the SARS-CoV-2 codon usage analysis as published here: https://academic.oup.com/ve/article/8/1/veac026/6553895. Please feel free to contact us if you have problems running our scripts at [email protected]
H-ESBCNs (Hidden Extended Suppes-Bayes Causal Networks). The manuscript of the method is available at: https://academic.oup.com/bioinformatics/article/38/3/754/6396863
OncoScore is a tool to measure the association of genes to cancer based on citation frequency in biomedical literature. The manuscript of the method is published on Scientific Reports and available at http://www.nature.com/articles/srep46290. The tool can also be used as a Web interface at https://www.galseq.com/next-generation-sequencing/oncoscore-software/.
RESOLVE (Robust EStimation Of mutationaL signatures Via rEgularization) is an R package for the the efficient extraction and assignment of mutational signatures from cancer genomes.
Extracting mutational signatures via LASSO. The manuscript of the method is published on PLOS Computational Biology and available at: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009119