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@BIMIB-DISCo

Data and Computational Biology Group UNIMIB (was BI*oinformatics MI*lan B*icocca)

The github organization of the DCB group of the DISCo, Università degli Studi di Milano Bicocca

Pinned

  1. J-Space.jl J-Space.jl Public

    J-SPACE is a Julia package to simulate the spatial growth and the genomic evolution of a cell population and the experiment of sequencing the genome of the sampled cells.

    Julia 6 1

  2. LACE 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 longitudin…

    R 14 4

  3. PMCE 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 pro…

    C 1 1

  4. TRaIT 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 1 2

  5. TRONCO 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 28 7

  6. VERSO 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 6 4

Repositories

Showing 10 of 42 repositories
  • SOPHYSM.jl Public Forked from niccolo99mandelli/SOPHYSM.jl

    SOPHYSM - SOlid tumors PHYlogenetic Spatial Modeller - Julia GUI for Histological Analysis and Cancer Simulation

    Julia 0 MIT 1 0 0 Updated May 31, 2024
  • JHistint.jl Public Forked from niccolo99mandelli/JHistint.jl

    Julia interface for implementing REST APIs available on the CDSA (Cancer Slide Digital Archive) portal for managing histological images available from TCGA. The library includes functions for managing image processing algorithms for cell segmentation, constructing the adjacency matrix, tessellation process and interfacing with J-Space.jl.

    Julia 0 MIT 1 0 0 Updated May 13, 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 6 4 0 0 Updated May 7, 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 28 GPL-3.0 7 0 0 Updated May 7, 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 14 GPL-3.0 4 0 0 Updated May 7, 2024
  • cyTRON-js Public

    A cytoscape-js application providing a front end and workflow management for the TRONCO R Suite.

    JavaScript 0 1 1 3 Updated Apr 30, 2024
  • J-Space.jl Public

    J-SPACE is a Julia package to simulate the spatial growth and the genomic evolution of a cell population and the experiment of sequencing the genome of the sampled cells.

    Julia 6 1 3 0 Updated Apr 8, 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 1 Apache-2.0 1 0 0 Updated Oct 17, 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 1 Apache-2.0 2 0 0 Updated Jun 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 1 2 0 0 Updated Jun 19, 2023
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