Repositories list

• CLAM

  Public
  Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering

  Python

  •

  GNU General Public License v3.0

  •351•0•1•0•Updated Oct 10, 2024Oct 10, 2024

• CINSignatureQuantification

  Public
  Quantifying copy number signatures from absolute copy number profiles

  R

  •

  Other

  •4•23•1•0•Updated Sep 13, 2024Sep 13, 2024

• slide-classifier

  Public
  Triage and Diagnosis of Cytosponge Histopathology

  Python

  •

  MIT License

  •0•0•0•0•Updated Aug 30, 2024Aug 30, 2024

• scAbsolute

  Public
  Measuring single-cell ploidy and cell cycle status in single-cell DNA sequencing data

  R

  •

  Other

  •3•3•1•1•Updated Aug 20, 2024Aug 20, 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 .png file) of the mask of where the tissue is located (black: tissue, white: background).

  Python

  •

  MIT License

  •1•7•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•0•0•0•Updated Jun 9, 2024Jun 9, 2024

• scDNAseq-workflow

  Public
  calling absolute copy numbers on single cell DNA sequencing data - stagging repo for public release

  R

  •2•3•0•0•Updated Apr 17, 2024Apr 17, 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

  •2•6•3•0•Updated Aug 30, 2023Aug 30, 2023

• Drews2022_CIN_Compendium

  Public
  Main repository for Drews et al. (Nature, 2022)

  HTML

  •

  Other

  •6•37•1•0•Updated Aug 14, 2023Aug 14, 2023

• CINSignatureDiscovery

  Public
  Discovering copy number signatures from TCGA and new cohorts.

  R

  •

  Other

  •2•7•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•17•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•0•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

  •27•0•0•1•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

  •4•21•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

  •5•49•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 Gehrung et al.

  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

• nem

  Public
  Local branch of bioconductor nested effect models package

  R

  •0•0•0•0•Updated Jan 28, 2020Jan 28, 2020

• SCperturb

  Public
  Data and analysis package for single cell perturbation data

  R

  •

  Other

  •0•2•0•0•Updated Oct 31, 2019Oct 31, 2019