Repositories list

• TRONCO

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

  algorithmstumorscancer-inference

  R

  •

  GNU General Public License v3.0

  •7•28•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•7•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•15•0•0•Updated Oct 31, 2024Oct 31, 2024

• SOPHYSM.jl

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

  Julia

  •

  MIT License

  •2•0•0•0•Updated Oct 18, 2024Oct 18, 2024

• JHistint.jl

  Public
  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

  •

  MIT License

  •1•0•0•0•Updated Oct 9, 2024Oct 9, 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.

  simulationcomputational-biologycancer-evolution

  Julia

  •

  Other

  •1•6•3•0•Updated Apr 8, 2024Apr 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

  •

  Apache License 2.0

  •1•1•0•0•Updated Oct 17, 2023Oct 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

  •

  Apache License 2.0

  •2•1•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•1•0•0•Updated Jun 19, 2023Jun 19, 2023

• scFBA

  Public
  MATLAB

  •5•6•5•1•Updated Mar 14, 2023Mar 14, 2023

• ENAD-experiments

  Public
  Python

  •0•2•0•0•Updated Nov 25, 2022Nov 25, 2022

• COSDEG

  Public
  R

  •1•0•0•0•Updated Sep 28, 2022Sep 28, 2022

• SARS-CoV-2-IHMV

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

  R

  •

  Apache License 2.0

  •1•3•0•0•Updated Aug 30, 2022Aug 30, 2022

• Mutational_Patterns

  Public
  R

  •0•0•0•0•Updated Jul 27, 2022Jul 27, 2022

• SARS-CoV-2-early-detection

  Public
  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: [email protected]

  R

  •0•0•0•0•Updated May 20, 2022May 20, 2022

• LACE-DEMO

  Public
  1•0•0•0•Updated Apr 10, 2022Apr 10, 2022

• Virasig

  Public
  Other

  •0•0•0•0•Updated Jan 18, 2022Jan 18, 2022

• LACEView

  Public
  A tool to visualize LACE output.

  visualizationcancerevolution+ 1longitudinal

  JavaScript

  •2•1•0•0•Updated Jan 9, 2022Jan 9, 2022

• OG-SPACE

  Public
  Public repository of OG-SPACE

  R

  •0•0•0•0•Updated Nov 17, 2021Nov 17, 2021

• FLUX-PREDICT

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated May 12, 2021May 12, 2021

• ProPhET

  Public
  Probabilistic PHylogeny Extraction Tool

  Julia

  •0•0•0•0•Updated Apr 12, 2021Apr 12, 2021

• DCB-Theme

  Public
  Beamer theme for DCBLab LaTeX slides

  TeX

  •0•0•0•0•Updated Apr 12, 2021Apr 12, 2021

• VERSO-UTILITIES

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

  Jupyter Notebook

  •

  Apache License 2.0

  •1•1•0•0•Updated Feb 26, 2021Feb 26, 2021

• MET-NET-CLASSIFICATION

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Dec 15, 2020Dec 15, 2020

• Accelerated-globalSA-of-constraint-based-models

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

  Python

  •1•0•0•0•Updated Nov 30, 2020Nov 30, 2020

• LACE-UTILITIES

  Public
  Utilities repository for LACE (Longitudinal Analysis of Cancer Evolution); main tool repository: https://github.com/BIMIB-DISCo/LACE

  R

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 17, 2020Oct 17, 2020

• closedLoop-CT4TD

  Public
  Python

  •0•0•0•0•Updated Aug 31, 2020Aug 31, 2020

• review-scRNA-seq-DENOISING

  Public
  Jupyter Notebook

  •3•5•2•0•Updated Jun 29, 2020Jun 29, 2020

• ANNAPD

  Public
  Artificial Neural Networks Activation Pattern Diagram

  Jupyter Notebook

  •0•0•0•0•Updated May 23, 2020May 23, 2020

• CT4TD

  Public
  Control Theory for Therapy Design

  Python

  •1•1•0•0•Updated Apr 14, 2020Apr 14, 2020