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Name: Markowetz lab @ CRUK Cambridge Institute

Type: Organization

Bio: Developing technologies for doctors to make better decisions faster

Location: Cambridge

Blog: http://www.markowetzlab.org

Markowetz lab @ CRUK Cambridge Institute's Projects

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.

biasedurn

Copy of the BiasedUrn Packaged. I simply changed MAXCOLORS from 32 to 50k

cinsignaturecelllines

Quantifying copy number signatures on cell lines

cinsignaturediscovery

Discovering copy number signatures from TCGA and new cohorts.

cinsignaturegenomesimulation

Simulating mutational processes to benchmark feature-based copy number signatures

cinsignaturequantification

Quantifying copy number signatures from absolute copy number profiles

cinsignatureswgsbinsize

Identification of optimal sWGS bin size to model SNP6 arrays

cnsignatures

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

cutter

3D printed tumor moulds for guided tissue sampling

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.

drews2022_cin_compendium

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

frenchfish

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

frenchfish_analyses

Analyses corresponding with the frenchFISH paper

geojson_xml

A tool to convert geojson files (e.g., used in QuPath) into xml files (e.g., used in ASAP) and vice versa.

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.

nem

Local branch of bioconductor nested effect models package

pancreaticcancerkras

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

pathml

A Python library for deep learning on whole-slide images

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.

qdnaseqmod

Modified QDNAseq package used in various markowetz repositories for sWGS absolute fitting

scabsolute

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

scdnaseq-workflow

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

scperturb

Data and analysis package for single cell perturbation data

scrna-seq_crispr_analysis

scRNA-Seq CRISPR Analysis code for Edwards et al

slidl

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

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.

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).

markowetzlab Goto Github PK

Markowetz lab @ CRUK Cambridge Institute's Projects

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