index.Rmd

---
title: "Home"
site: workflowr::wflow_site
output:
  workflowr::wflow_html:
    toc: false
---

This repository has example notebooks that demonstrate how to go from fastq files to sparse matrices for scRNA-seq data from start to end. To run the notebooks, please install [kallisto](https://pachterlab.github.io/kallisto/starting), [bustools](https://github.com/BUStools/bustools), and the [BUSpaRse](https://github.com/lambdamoses/BUSpaRse) R package. 

1. [10x v2 chemistry - 1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells](10xv2.html)
2. 10x v3 chemistry - 1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells (coming soon)

If you have problems with the notebooks, or have questions about them, please go to the [GitHub repo of this website](https://github.com/lambdamoses/BUSpaRse_notebooks).