Starred repositories
A curated list of awesome AI tools, libraries, papers, datasets, and frameworks that accelerate scientific discovery — from physics and chemistry to biology, materials, and beyond.
LARIS enables accurate and efficient ligand and receptor interaction analysis in spatial transcriptomics
Lab for quantitative bioimage analysis experiments in Python
Second-order spatial analysis for multiplex imaging data
Integrating GWAS and spatial transcriptomics for spatially resolved mapping of cells associated with human complex traits.
Integrated pipeline for multiplexed image analysis
A collection of scripts and tools for loading, processing, and handling single cell data.
Integrating histology and spatial transcriptomics - NeurIPS 2024
code for "An Integrated Clinical, Omic, and Image Atlas of an Evolving Metastatic Breast Cancer"
A python package for Multiomics and Ecological Spatial Analysis (MESA)
QuPath - Open-source bioimage analysis for research
Tools for empirical design of hybridization-based target enrichment probes for 3' single-cell RNA-seq
Workflows for pre-processing sequencing data from sequence census assays
Tools for sgRNA calling in direct capture Perturb-seq data
Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation
Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information for multiplexed in situ imaging data. No training dataset wi…
Combining multimodality histopathology images for integrated cancer research
This is the alpha version of the CellOracle package
Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms
TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUmaps can be used as a web service or locally in your computer,…
A pipeline to transform images into valuable analysis items