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

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

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

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

Community-provided extensions to Seurat

Analysis Pipeline for Single Cell ATAC-seq

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.

PhenoPixel: A web-based bioimage analysis platform for bacterial single-cell microscopy analytics.

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

Tutorial for scRNA-seq data analysis beginners using R

Scissor package

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

List of Spatial Transcriptomics related Tools organized per category

This repository contains scNotebooks, a collection of interactive Jupyter and Google Colab notebooks designed to teach and practice single‑cell and spatial transcriptomics. The notebooks guide learners through the complete workflow from introductory steps and single‑cell pipelines to diverse analytical approaches, and FAIR and sharing data

A collection of 50+ trajectory inference methods within a common interface 📥📤

Context specific and dynamic gene regulatory network reconstruction and analysis

Single Cell Analysis Pipelines

Cluster single cells and analyze cell clade relationships with colorful visualizations.

R package to visualize gene expression data based on weighted kernel density estimation

Spatial Single-Cell Analysis Toolkit