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 Repositories
J-Space.jl
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.
LACE
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.
oral_squamous_longitudinal
Utilities repository to analyze single-cell data from https://www.nature.com/articles/s41467-018-07261-3.
PiCnIc-COADREAD
PiCnIc implementation for COADREAD
PMCE
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
review-scRNA-seq-DENOISING
scFBA
TRaIT
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
TRONCO
Repository of the TRanslational ONCOlogy library, which includes various algorithms (such as CAPRESE and CAPRI) and the Pipeline for Cancer Inference (PICNIC).
VERSO
Viral Evolution ReconStructiOn (VERSO). The manuscript of the method is available at: https://www.cell.com/patterns/fulltext/S2666-3899(21)00022-2
Data and Computational Biology Group UNIMIB (was BI*oinformatics MI*lan B*icocca)'s Repositories
BIMIB-DISCo/TRONCO
Repository of the TRanslational ONCOlogy library, which includes various algorithms (such as CAPRESE and CAPRI) and the Pipeline for Cancer Inference (PICNIC).
BIMIB-DISCo/LACE
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/VERSO
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/J-Space.jl
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/scFBA
BIMIB-DISCo/review-scRNA-seq-DENOISING
BIMIB-DISCo/SARS-CoV-2-IHMV
Utilities repository to replicate the analyses presented in https://www.cell.com/iscience/fulltext/S2589-0042(21)00084-5
BIMIB-DISCo/ENAD-experiments
BIMIB-DISCo/CT4TD
Control Theory for Therapy Design
BIMIB-DISCo/LACEView
A tool to visualize LACE output.
BIMIB-DISCo/PMCE
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/TRaIT
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/VERSO-UTILITIES
Utilities repository for VERSO (Viral Evolution ReconStructiOn); main tool repository: https://github.com/BIMIB-DISCo/VERSO
BIMIB-DISCo/VirMutSig
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/Accelerated-globalSA-of-constraint-based-models
Accelerated global sensitivity analysis of genome-wide constraint-based metabolic models
BIMIB-DISCo/closedLoop-CT4TD
BIMIB-DISCo/OG-SPACE
Public repository of OG-SPACE
BIMIB-DISCo/ANNAPD
Artificial Neural Networks Activation Pattern Diagram
BIMIB-DISCo/COSDEG
BIMIB-DISCo/DCB-Theme
Beamer theme for DCBLab LaTeX slides
BIMIB-DISCo/FLUX-PREDICT
BIMIB-DISCo/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/LACE-DEMO
BIMIB-DISCo/LACE-UTILITIES
Utilities repository for LACE (Longitudinal Analysis of Cancer Evolution); main tool repository: https://github.com/BIMIB-DISCo/LACE
BIMIB-DISCo/MET-NET-CLASSIFICATION
BIMIB-DISCo/Mutational_Patterns
BIMIB-DISCo/ProPhET
Probabilistic PHylogeny Extraction Tool
BIMIB-DISCo/SARS-CoV-2-early-detection
In this repository we provide the code to replicate the early detection analysis of SARS-CoV-2 variants from deep sequencing samples. Please feel free to contact us if you have any question on the pipeline at: daniele.ramazzotti1@gmail.com
BIMIB-DISCo/SOPHYSM.jl
SOPHYSM - SOlid tumors PHYlogenetic Spatial Modeller - Julia GUI for Histological Analysis and Cancer Simulation
BIMIB-DISCo/Virasig