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:
Then, navigate to the repo directory and launch 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.