README.md

In Ghosn-Lab/BatchNorm: Data Matrix Normalization and Merging Strategies Minimize Batch-specific Systemic Variation in scRNA-Seq Data

Ghosn Laboratory

Data Matrix Normalization and Merging Strategies Minimize Batch-specific Systemic Variation in scRNA-Seq Data

This repository is intended to support reproducibility of our recent manuscript: "Data Matrix Normalization and Merging Strategies Minimize Batch-specific Systemic Variation in scRNA-Seq Data." The complete text and supplementary materials of the preprint are made freely available via bioRxiv.[1]

To enable rapid reproduction of the published figures, we have made a set of pre-assembled Seurat objects available as part of an R packaged "BatchNorm", available on github here.

Installation

To install the package (along with select published datasets in support of the manuscript) in R, run:

if(!requireNamespace("devtools", quietly = TRUE)) {
 install.packages("devtools") 
}
devtools::install_github("Ghosn-Lab/BatchNorm")

The package should install within a few minutes, and all functions can be reproduced on a standard desktop or laptop without special hardware.

Examples

To enable reproducibility, we have published this repository as a user-friendly website here. Anyone with access to R can reproduce the figures in our manuscript by following along with our vignettes here

References

[1] Babcock, B. R. et al. Data Matrix Normalization and Merging Strategies Minimize Batch-specific Systemic Variation in scRNA-Seq Data. bioRxiv (2021) DOI: https://doi.org/10.1101/2021.08.18.456898

Ghosn-Lab/BatchNorm documentation built on Dec. 17, 2021, 9:32 p.m.