PhantomPurgeR

R package for the optimal purging of phantom molecules by the robust estimation of the sample index hopping rate in multiplexed droplet-based single-cell RNA-seq data

Paper

Farouni, R., Djambazian, H., Ferri, L. E., Ragoussis, J., and Najafabadi, H. S. (2020). Model-based analysis of sample index hopping reveals its widespread artifacts in multiplexed single-cell RNA-sequencing. Nature Communications.

The bioRxiv preprint can be accessed here.

Website

The paper's website hosts code and R Markdown notebooks implementing the statistical modeling approach

Installation

In R run:

library("devtools")
devtools::install_github("csglab/PhantomPurgeR")

Installation Requirements

The code was tested using R 3.6.2 running on Ubuntu 18.04.2 LTS and R 3.5.2 running on CentOS Linux 7.

To run the code, the following R packages are required.

• rhdf5
• DropletUtils
• tidyverse
• matrixStats
• broom
• furrr
• tictoc
• data.table
• cowplot
• scales

Supplementary Data

Contact

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