Deep probabilistic analysis of single-cell and spatial omics data

Analysis of single cell RNA-seq data course

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

A list of scRNA-seq analysis tools

An interactive explorer for single-cell transcriptomics data

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

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

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

Single-cell Transcriptome and Regulome Analysis Pipeline

Papers with code for single cell related papers

Single cell perturbation prediction

Reference mapping for single-cell genomics

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

Spatial alignment of single cell transcriptomic data.

Simple simulation of single-cell RNA sequencing data

Single cell trajectory detection

A tool for semi-automatic cell type classification

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

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.