Skip to content

@ramazzottilab Translational Bioinformatics Laboratory

Change the repository type filter

All

    Repositories list

    15 repositories

    • OncoScore

      Public
      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.
      R
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Nov 1, 2024Nov 1, 2024

    • ASTUTE

      Public
      ASTUTE is an R package designed to integrate cancer genomic and transcriptomic data in order to perform genotype-phenotype mapping.
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated Nov 1, 2024Nov 1, 2024

    • RESOLVE

      Public
      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.
      R
      •
      Apache License 2.0
      •1•0•0•0•Updated Oct 31, 2024Oct 31, 2024

    • SparseSignatures

      Public
      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
      R
      •
      Apache License 2.0
      •5•0•0•0•Updated Oct 31, 2024Oct 31, 2024

    • VERSO

      Public
      Viral Evolution ReconStructiOn (VERSO). The manuscript of the method is available at: https://www.cell.com/patterns/fulltext/S2666-3899(21)00022-2
      R
      •4•0•0•0•Updated Oct 31, 2024Oct 31, 2024

    • TRONCO

      Public
      Repository of the TRanslational ONCOlogy library, which includes various algorithms (such as CAPRESE and CAPRI) and the Pipeline for Cancer Inference (PICNIC).
      R
      •
      GNU General Public License v3.0
      •8•0•0•0•Updated Oct 31, 2024Oct 31, 2024

    • LACE

      Public
      LACE 2.0 is a new release of the LACE R Bioconductor package, which provides an interactive user interface to perform clonal evolution analyses for single-cell sequencing data, including longitudinal experiments. The tool also allows to annotate and retrieve the relevant variants based on user-defined criteria.
      R
      •
      GNU General Public License v3.0
      •4•0•0•0•Updated Oct 31, 2024Oct 31, 2024

    • SIMLR

      Public
      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
      MATLAB
      •
      GNU General Public License v3.0
      •61•0•0•0•Updated Oct 31, 2024Oct 31, 2024

    • ASCETIC

      Public
      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. Preprint at https://www.nature.com/articles/s41467-023-41670-3
      R
      •
      Apache License 2.0
      •1•0•0•0•Updated Oct 31, 2024Oct 31, 2024

    • PMCE

      Public
      GitHub repository of the PMCE Framework. F. Angaroni, K. Chen, C. Damiani, G. Caravagna, A. Graudenzi, D. Ramazotti, PMCE: efficient inference of expressive models of cancer evolution with high prognostic power, Bioinformatics, 2021; btab717, https://doi.org/10.1093/bioinformatics/btab717
      C
      •
      Apache License 2.0
      •1•0•0•0•Updated Oct 17, 2023Oct 17, 2023

    • HESBCN

      Public
      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
      C
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Oct 17, 2023Oct 17, 2023

    • .github

      Public
      Welcome to the Translational Bioinformatics Laboratory (TBL) at the Department of Medicine and Surgery of the University of Milano-Bicocca, Milano, Italy!
      0•0•0•0•Updated Oct 2, 2023Oct 2, 2023

    • VirMutSig

      Public
      The VirMutSig protocol is available at: Maspero, D. et al. "VirMutSig: Discovery and assignment of viral mutational signatures from sequencing data", STAR Protocols 2.4 (2021): 100911. https://doi.org/10.1016/j.xpro.2021.100911
      R
      •
      Apache License 2.0
      •2•0•0•0•Updated Jun 19, 2023Jun 19, 2023

    • TRaIT

      Public
      Source code and input data to reproduce the case studies presented in the TRaIT framework: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2795-4
      R
      •2•0•0•0•Updated Jun 19, 2023Jun 19, 2023

    • CIMLR

      Public
      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
      MATLAB
      •
      GNU General Public License v3.0
      •7•0•0•0•Updated May 19, 2023May 19, 2023