Data and Computational Biology Group UNIMIB (was BI*oinformatics MI*lan B*icocca)
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Repositories
- SOPHYSM.jl Public Forked from niccolo99mandelli/SOPHYSM.jl
SOPHYSM - SOlid tumors PHYlogenetic Spatial Modeller - Julia GUI for Histological Analysis and Cancer Simulation
BIMIB-DISCo/SOPHYSM.jl’s past year of commit activity - 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
BIMIB-DISCo/VERSO’s past year of commit activity - TRONCO Public
Repository of the TRanslational ONCOlogy library, which includes various algorithms (such as CAPRESE and CAPRI) and the Pipeline for Cancer Inference (PICNIC).
BIMIB-DISCo/TRONCO’s past year of commit activity - 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.
BIMIB-DISCo/LACE’s past year of commit activity - 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.
BIMIB-DISCo/JHistint.jl’s past year of commit activity - 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.
BIMIB-DISCo/J-Space.jl’s past year of commit activity - 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
BIMIB-DISCo/PMCE’s past year of commit activity - 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
BIMIB-DISCo/VirMutSig’s past year of commit activity - 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
BIMIB-DISCo/TRaIT’s past year of commit activity - scFBA Public
BIMIB-DISCo/scFBA’s past year of commit activity
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