/singlecell

Primary LanguageJupyter Notebook

Introduction

singlecell_analyzer.ipynb is a general purpose notebook for clustering of 10X single-cell RNA-seq data as well as differential expression analysis. The notebook uses the scanpy API.

The conda environment I use for data science and single-cell analysis is in environment.yaml for reference. This environment has all the tools you need to run the notebook.

conda env create -f environment.yaml

conda activate datascience

jupyter lab