This repository provides code used to perform analyses presented in Comprehensive integration of single-cell data.

An open-access bioRxiv version of the manuscript can be found here.

All major components of the analysis can be reproduced using the Snakemake workfow provided in this repository. Please note that there is a substantial amount of data required to reproduce the entire analysis (over 100 Gb).

Individual plots can be reproduced by setting the snakemake target. For example, figure 2 of the paper can be reproduced by running:

snakemake figure2

All the available rules can be viewed in the snakemake file.

@article{,
  title    = "Comprehensive integration of single-cell data",
  author   = "Stuart, Tim and Butler, Andrew and Hoffman, Paul and Hafemeister,
              Christoph and Papalexi, Efthymia and Mauck, William M and Hao, Yuhan and
              Stoeckius, Marlon and Smibert, Peter and Satija, Rahul",
  journal  = "Cell",
  month    =  jun,
  year     =  2019,
  url      =  "https://doi.org/10.1016/j.cell.2019.05.031"
  language = "en"
}