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

Data and Computational Biology Group UNIMIB (was BIoinformatics MIlan B*icocca)'s repositories

TRONCO

Repository of the TRanslational ONCOlogy library, which includes various algorithms (such as CAPRESE and CAPRI) and the Pipeline for Cancer Inference (PICNIC).

Language:RGPL-3.028 13 79

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.

Language:RGPL-3.015 6 1

VERSO

Viral Evolution ReconStructiOn (VERSO). The manuscript of the method is available at: https://www.cell.com/patterns/fulltext/S2666-3899(21)00022-2

Language:R7 5 4

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.

Language:JuliaNOASSERTION6 6 3

scFBA

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review-scRNA-seq-DENOISING

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SARS-CoV-2-IHMV

Utilities repository to replicate the analyses presented in https://www.cell.com/iscience/fulltext/S2589-0042(21)00084-5

Language:RApache-2.03 6 1

ENAD-experiments

Language:Python2 60

CT4TD

Control Theory for Therapy Design

Language:Python1 30

LACEView

A tool to visualize LACE output.

Language:JavaScript1 50

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

Language:CApache-2.01 60

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

Language:R1 40

VERSO-UTILITIES

Utilities repository for VERSO (Viral Evolution ReconStructiOn); main tool repository: https://github.com/BIMIB-DISCo/VERSO

Language:Jupyter NotebookApache-2.01 50

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

Language:RApache-2.01 60

Accelerated-globalSA-of-constraint-based-models

Accelerated global sensitivity analysis of genome-wide constraint-based metabolic models

Language:Python060

closedLoop-CT4TD

Language:Python040

OG-SPACE

Public repository of OG-SPACE

Language:R060

ANNAPD

Artificial Neural Networks Activation Pattern Diagram

Language:Jupyter Notebook040

COSDEG

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DCB-Theme

Beamer theme for DCBLab LaTeX slides

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FLUX-PREDICT

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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.

Language:JuliaMIT000

Data and Computational Biology Group UNIMIB (was BIoinformatics MIlan B*icocca)

BIMIB-DISCo