Single-Cell RNA-seq Analysis Notebooks


Single-Cell RNA-seq Clustering Analysis Notebook

This notebook is published in: https://f1000research.com/articles/7-1306/v2

The goal of this notebook is to provide a standard single-cell RNA-seq analysis workflow for pre-processing, identifying sub-populations of cells by clustering, and exploring biomarkers to explain intra-population heterogeneity. The workflow is modeled after the Seurat Guided Clustering Tutorial and performs all analyses using the scanpy library.

Census of Immune Cells: Single-Cell Workflow with CoGAPS

This notebook identifies immune cell types by clustering single-cell RNA-seq data using R and Python to run non-negative matrix factorization.