Last updated: 2019-02-02

workflowr checks: (Click a bullet for more information)
Expand here to see past versions:

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")

This is work in progress. This package will be on Bioconductor soon.

Installation note for MacOS

In case you encounter this error during installation:

clang: error: unsupported option '-fopenmp'

This is what to do to resolve it:

This package contains compiled code, and a compiler that supports OpenMP is required to compile this package. However, the default clang that comes with MacOS does not support OpenMP. MacOS users using R 3.5 should download and install Clang 6.0 and gfortran 6.1 compilers from this webpage from CRAN, which has OpenMP enabled. R 3.5 no longer works with Clang 4, which was used for R 3.4.

Then, if the file ~/.R/Makevars does not exist, in the terminal, go to your home directory by cd, use mkdir .R to create the .R directory, and type vim Makevars to create and start editing the file. If it already exists, then type vim Makevars to edit it.

Alternatively, if you are uncomfortable with the command line, this can be done in RStudio. First use file.exists("~/.R/Makevars") to check if ~/.R/Makevars exists. Then use dir.exists("~/.R") to check that if the ~/.R directory exists. If it does not, then use dir.create("~/.R") to create the directory. Then use file.create("~/.R/Makevars") to create that file. Then navigate to that file in the Files pane in RStudio, open that file in RStudio, and edit it.

Add the following to the ~/.R/Makevars file:

CXX= /usr/local/clang6/bin/clang++  -Wall
CXX1X= /usr/local/clang6/bin/clang++
CXX98= /usr/local/clang6/bin/clang++
CXX11= /usr/local/clang6/bin/clang++
CXX14= /usr/local/clang6/bin/clang++
CXX17= /usr/local/clang6/bin/clang++

Above is the default path where this Clang 6.0 is installed. Please change it if Clang 6.0 is installed in a custom path. This will tell R to use the Clang 6.0 from CRAN that has OpenMP enabled. Then restart the R session and reinstall this package.


  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, have questions about them, or want to download the notebooks, please go to the GitHub repo of this website.

This reproducible R Markdown analysis was created with workflowr 1.1.1