danro9685
Department of Medicine and Surgery, University of Milano-Bicocca, Milano, Italy
University of Milano-Bicocca, Milano, ItalyMilano, Italy
Pinned Repositories
SIMLR
Implementations in both Matlab and R of the SIMLR method. The manuscript of the method is available at: https://www.nature.com/articles/nmeth.4207
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
Mutational signature analysis for the BRCA project.
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
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 daniele.ramazzotti1@gmail.com
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
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.
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
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
ASTUTE
ASTUTE is an R package designed to integrate cancer genomic and transcriptomic data in order to perform genotype-phenotype mapping.
danro9685's Repositories
danro9685/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
danro9685/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
danro9685/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
danro9685/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.
danro9685/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
danro9685/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.
danro9685/BRCA
Mutational signature analysis for the BRCA project.
danro9685/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 daniele.ramazzotti1@gmail.com