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@markowetzlab Markowetz lab @ CRUK Cambridge Institute

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    33 repositories

    • r-swgs-absolutecn

      Public
      R package for functions used in swgs-absolutecn
      R
      •
      Other
      •0•1•0•0•Updated Jul 28, 2026Jul 28, 2026

    • sc_analysis

      Public
      Single-cell copy-number analysis pipelines for auditable post-scAbsolute QC and post-scUnique evolutionary visualization.
      R
      •0•0•0•0•Updated Jul 22, 2026Jul 22, 2026

    • scDNAseq-workflow

      Public
      calling absolute copy numbers on single cell DNA sequencing data - stagging repo for public release
      R
      •5•6•0•0•Updated Jul 21, 2026Jul 21, 2026

    • scAbsolute

      Public
      Measuring single-cell ploidy and cell cycle status in single-cell DNA sequencing data
      R
      •
      Other
      •4•7•0•0•Updated Jul 21, 2026Jul 21, 2026

    • CINSignatureQuantification

      Public
      Quantifying copy number signatures from absolute copy number profiles
      R
      •
      Other
      •6•29•1•0•Updated Jul 23, 2025Jul 23, 2025

    • snakemake-SPRINTER

      Public
      snakemake workflow to run SPRINTER
      C++
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jul 10, 2025Jul 10, 2025

    • slide-classifier

      Public
      Triage and Diagnosis of Cytosponge Histopathology
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 10, 2024Dec 10, 2024

    • BiasedUrn

      Public
      Copy of the BiasedUrn Packaged. I simply changed MAXCOLORS from 32 to 50k
      C++
      •0•0•0•0•Updated Jul 30, 2024Jul 30, 2024

    • tissue_segmentation

      Public
      This script takes whole slide images (typically .svs or .ndpi files; either from biospsies or Cytosponge etc) as an input and returns an image file (typically .…
      Python
      •
      MIT License
      •2•9•0•0•Updated Jul 22, 2024Jul 22, 2024

    • geojson_xml

      Public
      A tool to convert geojson files (e.g., used in QuPath) into xml files (e.g., used in ASAP) and vice versa.
      Python
      •1•6•0•0•Updated Jun 9, 2024Jun 9, 2024

    • CNsignatures

      Public
      This is data and code from our first paper on copy number signatures (Macintyre et al., Nat Gen, 2018).
      HTML
      •
      MIT License
      •1•7•3•0•Updated Aug 30, 2023Aug 30, 2023

    • Drews2022_CIN_Compendium

      Public
      Main repository for Drews et al. (Nature, 2022)
      HTML
      •
      Other
      •6•43•1•0•Updated Aug 14, 2023Aug 14, 2023

    • CINSignatureDiscovery

      Public
      Discovering copy number signatures from TCGA and new cohorts.
      R
      •
      Other
      •2•10•1•1•Updated Feb 3, 2023Feb 3, 2023

    • slidl

      Public
      A Python library of pre- and post-processing tools for applying deep learning to whole-slide images
      Python
      •
      GNU General Public License v3.0
      •2•22•0•0•Updated Jan 16, 2023Jan 16, 2023

    • Athena

      Public
      Single Cell CRISPR Screen
      Python
      •
      MIT License
      •0•2•0•0•Updated Sep 2, 2022Sep 2, 2022

    • QDNAseq.hg38

      Public
      QDNAseq bin annotation for hg38
      R
      •
      GNU General Public License v3.0
      •5•1•0•0•Updated Aug 10, 2022Aug 10, 2022

    • CINSignatureCellLines

      Public
      Quantifying copy number signatures on cell lines
      R
      •
      Other
      •0•1•0•0•Updated Jun 27, 2022Jun 27, 2022

    • CINSignatureSWGSBinsize

      Public
      Identification of optimal sWGS bin size to model SNP6 arrays
      R
      •
      Other
      •0•0•1•0•Updated Jun 24, 2022Jun 24, 2022

    • QDNAseqmod

      Public
      Modified QDNAseq package used in various markowetz repositories for sWGS absolute fitting
      R
      •34•0•1•0•Updated Jun 24, 2022Jun 24, 2022

    • CINSignatureGenomeSimulation

      Public
      Simulating mutational processes to benchmark feature-based copy number signatures
      R
      •
      Other
      •0•0•0•0•Updated Jun 9, 2022Jun 9, 2022

    • scRNA-Seq_CRISPR_analysis

      Public
      scRNA-Seq CRISPR Analysis code for Edwards et al
      Jupyter Notebook
      •0•0•0•0•Updated Jun 8, 2022Jun 8, 2022

    • barretts-segment-length-predictor

      Public
      Code to reproduce the analyses of "Automated quantification of Barrett's esophagus from non-endoscopic device predicts Barrett's segment length" by Berman et al…
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated May 29, 2022May 29, 2022

    • slidl-tutorial

      Public
      A tutorial demonstration of SliDL on an example dataset for the manuscript "SliDL: a toolbox for processing whole-slide images in deep learning" by Berman et al…
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•3•1•0•Updated Feb 14, 2022Feb 14, 2022

    • pathml-tutorial

      Public
      A tutorial demonstration of pathml on an example dataset for the manuscript "PathML: A unified framework for WSI analysis with deep learning" by Berman et al.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •5•24•4•0•Updated Feb 8, 2022Feb 8, 2022

    • PancreaticCancerKRAS

      Public
      Master Regulators of Oncogenic KRAS Response in Pancreatic Cancer: An Integrative Network Biology Analysis
      1•1•0•0•Updated Jan 11, 2022Jan 11, 2022

    • pathml

      Public
      A Python library for deep learning on whole-slide images
      Python
      •
      GNU General Public License v3.0
      •9•52•0•0•Updated Nov 5, 2021Nov 5, 2021

    • MULTIPLAI

      Public
      This is the repository for the manuscript "Predictive Modelling of Highly Multiplexed Tumour Tissue Images by Graph Neural Networks" by Martin-Gonzalez et al.
      Jupyter Notebook
      •1•5•0•0•Updated Aug 3, 2021Aug 3, 2021

    • cytosponge-triage

      Public
      This repository contains the source code for the manuscript titles 'Triage-driven diagnosis for early detection of esophageal cancer using deep learning' by Geh…
      Jupyter Notebook
      •6•8•2•0•Updated Jan 25, 2021Jan 25, 2021

    • frenchFISH_analyses

      Public
      Analyses corresponding with the frenchFISH paper
      R
      •0•0•0•0•Updated Oct 16, 2020Oct 16, 2020

    • frenchFISH

      Public
      Poisson models for quantifying DNA copy-number from fluorescence in situ hybridisation of tissue sections
      R
      •0•2•0•0•Updated Jun 25, 2020Jun 25, 2020
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