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    23 repositories

    • nf-fragmentomics

      Public
      NF-FRAGMENTOMICS PIPELINE
      Nextflow
      •
      MIT License
      •0•0•2•0•Updated Jan 30, 2025Jan 30, 2025

    • midaa

      Public
      Multiomics Deep Archetypal Analysis
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Jan 14, 2025Jan 14, 2025

    • FORECAST_image_tiling

      Public
      Pipelines used to convert CZI format slide images into a tiled JPEG format for downstream analysis
      Java
      •0•2•0•0•Updated Sep 20, 2024Sep 20, 2024

    • FORECAST_gleason_analysis

      Public
      Code for analysing the output of the Gleason segmentation pipeline as part of the whole slide analysis detailed in the paper "Tumor evolution metrics predict recurrence beyond 10 years in locally advanced prostate cancer" by Fernandez-Mateos, Cresswell, Trahearn, et al.
      MATLAB
      •
      MIT License
      •0•1•0•0•Updated Sep 20, 2024Sep 20, 2024

    • FORECAST_cell_classification

      Public
      The whole slide image cell classification pipeline used in the paper "Tumor evolution metrics predict recurrence beyond 10 years in locally advanced prostate cancer" by Fernandez-Mateos, Cresswell, Trahearn, et al.
      MATLAB
      •
      MIT License
      •0•3•0•0•Updated Sep 20, 2024Sep 20, 2024

    • FORECAST_gleason_segmentation

      Public
      The semantic segmentation pipeline used to perform Gleason segmentation of whole slide images in the paper "Tumor evolution metrics predict recurrence beyond 10 years in locally advanced prostate cancer" by Fernandez-Mateos, Cresswell, Trahearn, et al.
      Python
      •
      MIT License
      •1•4•0•0•Updated Sep 20, 2024Sep 20, 2024

    • nf-SOPRANO

      Public
      nextflow SOPRANO pipeline
      Nextflow
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 10, 2024Jun 10, 2024

    • FORECAST_low_pass_analysis

      Public
      R
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated May 29, 2024May 29, 2024

    • FORECAST_targeted_seq_analysis

      Public
      R
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated May 29, 2024May 29, 2024

    • epigenetic_heritability_and_cell_plasticity_reproducibility

      Public
      A repo with the scripts to reproduce the analysis in Oliveira et al. 2024
      R
      •
      MIT License
      •0•0•0•0•Updated May 1, 2024May 1, 2024

    • midaa_reproducibility

      Public
      A repository to store the code to reproduce the results in "Interpretable Multi-Omics Data Integration with Deep Archetypal Analysis"
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Apr 23, 2024Apr 23, 2024

    • pks_ecoli_figs

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 29, 2023Jun 29, 2023

    • EPICC2021_data_analysis_EPIGENOME

      Public
      Scripts used to analyse EPICC ATAC-Seq data
      R
      •1•8•0•0•Updated Feb 11, 2023Feb 11, 2023

    • EPICC2021_inference

      Public
      R
      •0•0•1•0•Updated Feb 11, 2023Feb 11, 2023

    • EPICC2021_data_analysis_RNA

      Public
      1•6•0•0•Updated Sep 23, 2022Sep 23, 2022

    • EPICC_shiny_app

      Public
      EPICC 2021 - ATAC-seq peak track visualisation (Shiny App)
      R
      •0•1•0•0•Updated Jun 15, 2022Jun 15, 2022

    • letter_Dentro_et_al_2021

      Public
      Code used to generate figures and results for the response to Dentro et al. 2021
      HTML
      •0•0•0•0•Updated May 26, 2022May 26, 2022

    • mobster_supp_data

      Public
      Supplementary Data released with Caravagna et al. Subclonal reconstruction of tumors by using machine learning and population genetics. Nature Genetics volume 52, 898–907(2020).
      HTML
      •2•3•0•0•Updated Sep 10, 2020Sep 10, 2020

    • mobster

      Public
      Model-based subclonal deconvolution from bulk sequencing.
      R
      •
      GNU General Public License v3.0
      •8•6•0•0•Updated Jun 25, 2020Jun 25, 2020

    • ExpEvolutionSteering

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated Feb 26, 2020Feb 26, 2020

    • MCMC-MutationalDistances-

      Public
      R
      •0•2•0•0•Updated Feb 5, 2020Feb 5, 2020

    • CHESS.cpp

      Public
      C++
      •0•1•0•0•Updated Feb 5, 2020Feb 5, 2020

    • revolver

      Public
      REVOLVER - Repeated Evolution in Cancer
      R
      •25•1•0•0•Updated Jan 12, 2020Jan 12, 2020