Join subcellular Visium HD bins into cells

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

Spatially-aware quality control for spatial transcriptomics

Detect doublets in single-cell RNA-seq data

PROST: A quantitative pattern recognition framework for spatial transcriptomics.

Spatially resolved transcriptomic analysis

Methods for detecting doublets in single-cell sequencing data

Spatial alignment of single cell transcriptomic data.

SRA Tools

R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data

StarDist - Object Detection with Star-convex Shapes

Repository for ENACT pipeline for end-to-end analysis of Visium HD data

plotthis is an R package that is built upon ggplot2 and other plotting packages.

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

Single Cell Consensus Clustering with Speed

Single-cell analysis in Python. Scales to >100M cells.

This is the development home of the workflow management system Snakemake. For general information, see

pathway based data integration and visualization

Data-driven Network-based Bayesian Inference of Drivers

Pretty heatmaps

Python bindings for SingleR

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

Differential expression of RNA-seq data using the Negative Binomial

scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing and spatial data in an easy and efficient way.