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index.Rmd
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---
title: "Home"
site: workflowr::wflow_site
output:
workflowr::wflow_html:
toc: false
---
# kallisto | bustools R notebooks
This repository has example notebooks that demonstrate usage of [`kallisto bus`](https://www.biorxiv.org/content/10.1101/673285v1) to generate gene count or transcript compatibility count (TCC) matrices from FASTQ files and some basic downstream analyses. 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/BUStools/BUSpaRse) R package.
## Notebooks
<div class = "row">
<div class = "col-md-6">
<center>
[![](https://bustools.github.io/BUS_notebooks_R/figure/10xv2.Rmd/tsne-1.png){width=600px}](https://bustools.github.io/BUS_notebooks_R/10xv2.html)
[1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells (10x v2 chemistry); demonstration of `bustools`](https://bustools.github.io/BUS_notebooks_R/10xv2.html)
</center>
</div>
<div class = "col-md-6">
<center>
[![](https://bustools.github.io/BUS_notebooks_R/figure/10xv3.Rmd/tsne-1.png){width=600px}](https://bustools.github.io/BUS_notebooks_R/10xv3.html)
[1k PBMCs from a Healthy Donor (10x v3 chemistry); demonstration of `TENxBUSData` and `BUSpaRse`](https://bustools.github.io/BUS_notebooks_R/10xv3.html)
</center>
</div>
</div>
<div class = "row">
<div class = "col-md-6">
<center>
[![](https://bustools.github.io/BUS_notebooks_R/figure/monocle2.Rmd/traj1-1.png){width=600px}](https://bustools.github.io/BUS_notebooks_R/monocle2.html)
[Monocle 2 pseudotime analysis with 10k E18 mouse neurons from 10x](https://bustools.github.io/BUS_notebooks_R/monocle2.html)
</center>
</div>
<div class = "col-md-6">
<center>
[![](https://bustools.github.io/BUS_notebooks_R/figure/monocle3.Rmd/ti-1.png){width=600px}](https://bustools.github.io/BUS_notebooks_R/monocle3.html)
[Monocle 3 pseudotime analysis with 10k E18 mouse neurons from 10x](https://bustools.github.io/BUS_notebooks_R/monocle3.html)
</center>
</div>
</div>
<div class = "row">
<div class = "col-md-6">
<center>
[![](https://bustools.github.io/BUS_notebooks_R/figure/slingshot.Rmd/lin2-1.png){width=600px}](https://bustools.github.io/BUS_notebooks_R/slingshot.html)
[Slingshot pseudotime analysis with 10k E18 mouse neurons from 10x](https://bustools.github.io/BUS_notebooks_R/slingshot.html)
</center>
</div>
<div class = "col-md-6">
[![](https://bustools.github.io/BUS_notebooks_R/figure/velocity.Rmd/v1b-1.png){width=600px}](https://bustools.github.io/BUS_notebooks_R/velocity.html)
[RNA velocity analysis with 10k E18 mouse neurons from 10x](https://bustools.github.io/BUS_notebooks_R/velocity.html)
</div>
</div>
-----------
Differential expression with equivalence classes in TCC matrix (coming soon)