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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.

pathml

A Python library for deep learning on whole-slide images

Python

Drews2022_CIN_Compendium

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

HTML

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.

Jupyter Notebook

CINSignatureQuantification

Quantifying copy number signatures from absolute copy number profiles

slidl

A Python library of pre- and post-processing tools for applying deep learning to whole-slide images

Python

cytosponge-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.

Jupyter Notebook

CNsignatures

This is data and code from our first paper on copy number signatures (Macintyre et al., Nat Gen, 2018).

HTML

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).

Python

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.

Jupyter Notebook

cutter

3D printed tumor moulds for guided tissue sampling

MATLAB

scAbsolute

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

Athena

Single Cell CRISPR Screen

Python

SCperturb

Data and analysis package for single cell perturbation data

scDNAseq-workflow

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

frenchFISH

Poisson models for quantifying DNA copy-number from fluorescence in situ hybridisation of tissue sections

PancreaticCancerKRAS

Master Regulators of Oncogenic KRAS Response in Pancreatic Cancer: An Integrative Network Biology Analysis

CINSignatureGenomeSimulation_TEMP

Simulation of processes of chromosomal instability on a chromosome and genome level

CINSignatureQuantification_TEMP

Enabling researchers to quantify pan-cancer copy number signatures on their copy number profiles

CINSignatureDiscovery_TEMP

Repo to detail how the pan-cancer copy number signatures were obtained from TCGA SNP6 arrays

barretts-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.

Jupyter Notebook

markowetzlab/slidl-tutorial

markowetzlab

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