Single-Cell RNA-sequencing

This repository contains a notebook demonstrating a pipeline for Single-cell RNA-sequencing data analysis. It comprises techniques such as dimensionality reduction and clustering.

Setup

This code was tested with Python version 3.9.12. To create a Python environment with conda, use:

conda create -n sc python=3.9.12

Then activate the environment with:

conda activate sc

With the environment activated, run the following command from the root directory of this project to install requirements:

pip install -r requirements.txt

To run the code, you may use an IDE like VSCode, or run the command below to open in Jupyter Lab:

jupyter-lab

To stop the running environment, just press Ctrl+C twice on the terminal.