Deep probabilistic analysis of single-cell and spatial omics data

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Analysis of single cell RNA-seq data course

An interactive explorer for single-cell transcriptomics data

A list of scRNA-seq analysis tools

Fast, sensitive and accurate integration of single-cell data with Harmony

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

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

Reference mapping for single-cell genomics

A tool for semi-automatic cell type classification

Table of software for the analysis of single-cell RNA-seq data.

Useful functions to make your scRNA-seq plot more cool!

Single-cell Transcriptome and Regulome Analysis Pipeline

Papers with code for single cell related papers

Single cell perturbation prediction

Spatial alignment of single cell transcriptomic data.

Single cell trajectory detection

R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

muon is a multimodal omics Python framework

Simple simulation of single-cell RNA sequencing data