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

Spatial Single Cell Analysis in Python

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

High dimensional weighted gene co-expression network analysis

Tools for computational pathology

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

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

Integrating histology and spatial transcriptomics - NeurIPS 2024

Spatiotemporal modeling of spatial transcriptomics

A framework for building evolvable, distributed, and general-purpose multi-agent system.

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

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

Bayesian Segmentation of Spatial Transcriptomics Data

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

A Toolbox for Spatial Transcriptomics Analysis

a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles

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

List of Spatial Transcriptomics related Tools organized per category

Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling"

Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab

Code for the spatialLIBD R/Bioconductor package and shiny app

"Orchestrating Spatial Transcriptomics Analysis with Bioconductor" (OSTA) online book

From geospatial to spatial -omics

Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project

Spatial-Linked Alignment Tool

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

Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities