Profile purification of single-cell spatial transcriptomics data

Tumor Landscape Analysis: An Ecologically Informed Framework to Understand Tumor Micro-environments

A novel machine learning pipeline to analyse spatial transcriptomics data

This repository contains the code used to generate figures and perform analysis for the manuscript titled "Transcriptomic and Spatial Proteomic Profiling Reveals the Cellular Composition and Spatia…

Tools for single-cell data processing

an integrative analysis tool for analysing large-scale single cell RNA-sequencing data

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

Efficient and precise single-cell reference atlas mapping with Symphony

IMC_Denoise: a software package to enhance Imaging Mass Cytometry.

Multiple-choice microscopy pipeline

NicheNet: predict active ligand-target links between interacting cells

Dockerized multi-channel image processing framework

This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.

An awk-like VCF parser