spatial-transcriptomics

Spatial Single Cell Analysis in Python

A general, evolvable, and distributed agent framework & harness for data science.

Tools for computational pathology

DANCE: a deep learning library and benchmark platform for single-cell analysis

Spatiotemporal modeling of spatial transcriptomics

Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc.)

Python package to perform enrichment analysis from omics data.

SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network

Integrating GWAS and spatial transcriptomics for spatially resolved mapping of cells associated with human complex traits.

List of Spatial Transcriptomics related Tools organized per category

Conversational & memory-enabled AI research partner for multi-omics analysis. CLI + Desktop App (installers in Releases). From biological idea to full research paper.

Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many other features.

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.

Spatial-Linked Alignment Tool

Construction of a 3D whole organism spatial atlas by joint modeling of multiple slices

Spatial omics in the browser for hundreds of images at once | 10x, IMC, IF, H&E, CosMX, & more | https://rakaia.io/

scCellFie infers metabolic activities from single-cell and spatial transcriptomics and offers a variety of downstream analyses.

Accurate and fast cell marker gene identification with COSG

Autonomous multi-agent framework to optimize scientific software

A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data