alexisvdb / Singlecellhaystack

singleCellHaystack

singleCellHaystack is a package for predicting differentially expressed genes (DEGs) in single cell transcriptome data. It does so without relying on clustering of cells into arbitrary clusters! Single-cell RNA-seq (scRNA-seq) data is often processed to fewer dimensions using Principal Component Analysis (PCA) and represented in 2-dimensional plots (e.g. t-SNE or UMAP plots). singleCellHaystack uses Kullback-Leibler Divergence to find genes that are expressed in subsets of cells that are non-randomly positioned in a these multi-dimensional spaces or 2D representations.

Citation

Our manuscript describing singleCellHaystack has been published in Nature Communications.

If you use singleCellHaystack in your research please cite our work using:

Vandenbon A, Diez D (2020). “A clustering-independent method for finding differentially expressed genes in single-cell transcriptome data.” Nature Communications, 11(1), 4318. doi: 10.1038/s41467-020-17900-3 (URL: https://doi.org/10.1038/s41467-020-17900-3).

Documentation and Demo

Our documentation includes a few example applications showing how to use our package:

• Toy example
• Multi-dimensional coordinates
• Advanced mode on multi-dimensional coordinates
• Spatial transcriptomics
• MOCA 100k cells
• 2D t-SNE coordinates
• Advanced mode on 2D t-SNE coordinates

Installation

You can install the released version of singleCellHaystack from CRAN with:

install.packages("singleCellHaystack")

You can also install singleCellHaystack from the GitHub repository as shown below. Typical installation times should be less than 1 minute.

require(remotes)
remotes::install_github("alexisvdb/singleCellHaystack")

System Requirements

Hardware Requirements

singleCellHaystack requires only a standard computer with sufficient RAM to support running R or RStudio. Memory requirements depend on the size of the input dataset.

Software Requirements

This package has been tested on Windows (Windows 10), macOS (Mojave 10.14.1 and Catalina 10.15.1), and Linux (CentOS 6.9 and Ubuntu 19.10).

singleCellHaystack depends on the following packages: splines (3.6.0), ggplot2 (3.2.0), reshape2 (1.4.3).