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callback (Calibrated Clustering via Knockoffs) Reproducibility

Introduction

We hope to make it as simple as possible to reproduce the results found in A knockoff calibration method to avoid over-clustering in single-cell RNA-sequencing. To that end, we have organized our analysis scripts as a series of R vignettes in this repository.

Reproducing Figures from the callback manuscript

Clone the repository:

git clone https://github.com/lcrawlab/callbackreproducibility

Then, navigate to the repo directory and launch R

cd callbackreproducibility
R

You can build the entire website using the following line of R code.

pkgdown::build_site()

Note that each Rmarkdown file is not fully run by R by default. To properly run an an Rmarkdown file run during the website building process, you need to remove

knitr::opts_chunk$set(eval = FALSE)

from the file header. We do not recommend doing this for the vignettes that actually use callback, sc-SHC, and CHOIR for clustering because they have a long runtime. Rather, the R portions of these files should be put in a script and run using Rscript.

Relevant Citations

callback is currently on the bioRxiv, here.

A. DenAdel, M. Ramseier, A. Navia, A. Shalek, S. Raghavan, P. Winter, A. Amini, and L. Crawford. A knockoff calibration method to avoid over-clustering in single-cell RNA-sequencing. bioRxiv.

Questions and Feedback

For questions or concerns with callbackreproducibility or the callback R package, please contact Alan DenAdel or Lorin Crawford. Any feedback on the manuscript or figure reproducibility is greatly appreciated.