PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)

🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.

List of Spatial Transcriptomics related Tools organized per category

Context specific and dynamic gene regulatory network reconstruction and analysis

Single Cell Analysis Pipelines

Spatial Single-Cell Analysis Toolkit

scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images

Spatial-Linked Alignment Tool

An implementation of MNN (Mutual Nearest Neighbors) correct in python.

Accurate and fast cell marker gene identification with COSG

ChatCell: Facilitating Single-Cell Analysis with Natural Language

Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.

Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

A spatial omics data analysis tool that enables both unsupervised and supervised discovery of complex tissue cellular neighborhoods from cell phenotypes.

<<------ Use SnapATAC!!

Reliable, scalable, efficient demultiplexing for single-cell RNA sequencing

scPretrain: Multi-task self-supervised learning for cell type classification

Spatial Multiomics Profiler for Spatial Characterization of Tissue Microenvironment (https://smprofiler.io)

SIMBA: SIngle-cell eMBedding Along with features