Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

Spatial Single Cell Analysis in Python

High dimensional weighted gene co-expression network analysis

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

Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

Tools for computational pathology

Integrating histology and spatial transcriptomics - NeurIPS 2024

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

Spatiotemporal modeling of spatial transcriptomics

Python package to perform enrichment analysis from omics data.

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

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

Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome

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

Bayesian Segmentation of Spatial Transcriptomics Data

List of Spatial Transcriptomics related Tools organized per category

A Toolbox for Spatial Transcriptomics Analysis

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.