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pathml
A Python library for deep learning on whole-slide imagesDrews2022_CIN_Compendium
Main repository for Drews et al. (Nature, 2022)pathml-tutorial
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.CINSignatureQuantification
Quantifying copy number signatures from absolute copy number profilesslidl
A Python library of pre- and post-processing tools for applying deep learning to whole-slide imagescytosponge-triage
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.CNsignatures
This is data and code from our first paper on copy number signatures (Macintyre et al., Nat Gen, 2018).tissue_segmentation
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).CINSignatureDiscovery
Discovering copy number signatures from TCGA and new cohorts.MULTIPLAI
This is the repository for the manuscript "Predictive Modelling of Highly Multiplexed Tumour Tissue Images by Graph Neural Networks" by Martin-Gonzalez et al.slidl-tutorial
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.cutter
3D printed tumor moulds for guided tissue samplingscAbsolute
Measuring single-cell ploidy and cell cycle status in single-cell DNA sequencing dataAthena
Single Cell CRISPR ScreenSCperturb
Data and analysis package for single cell perturbation datascDNAseq-workflow
calling absolute copy numbers on single cell DNA sequencing data - stagging repo for public releasefrenchFISH
Poisson models for quantifying DNA copy-number from fluorescence in situ hybridisation of tissue sectionsPancreaticCancerKRAS
Master Regulators of Oncogenic KRAS Response in Pancreatic Cancer: An Integrative Network Biology AnalysisCINSignatureGenomeSimulation_TEMP
Simulation of processes of chromosomal instability on a chromosome and genome levelCINSignatureQuantification_TEMP
Enabling researchers to quantify pan-cancer copy number signatures on their copy number profilesbarretts-segment-length-predictor
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.Love Open Source and this site? Check out how you can help us