Last updated: 2018-12-14

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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, bustools, and the BUSpaRse R package.

Installation of BUSpaRse

You can install BUSpaRse with:

if (!require(devtools)) install.packages("devtools")
devtools::install_github("BUStools/BUSpaRse")

This is work in progress. I’m trying to get this package to Bioconductor.

Notebooks

  1. 10x v2 chemistry - 1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells
  2. 10x v3 chemistry - 1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells

If you have problems with the notebooks, or have questions about them, please go to the GitHub repo of this website.


This reproducible R Markdown analysis was created with workflowr 1.1.1