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Daniele Ramazzotti's Projects

ascetic icon ascetic

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

brca icon brca

Mutational signature analysis for the BRCA project.

cimlr icon cimlr

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

codon_usage icon codon_usage

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]

hesbcn icon hesbcn

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 icon oncoscore

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 icon resolve

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.

sparsesignatures icon sparsesignatures

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

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