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. This package will be on Bioconductor soon.

Installation note: This package contains compiled code. MacOS users using R 3.5 should download and install Clang 6.0 and gfortran 6.1 compilers from this webpage. R 3.5 no longer works with Clang 4, which was used for R 3.4.

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

Notebooks for Drop-seq and CEL-seq2 are coming soom.

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