Reconstructing the Regulatory Programs of Target Genes in scRNA-Seq Data

Implementation of the scregclust algorithm described in Larsson, Held, et al. (2024) which reconstructs regulatory programs of target genes in scRNA-seq data. Target genes are clustered into modules and each module is associated with a linear model describing the regulatory program.

Single-cell Regulatory-driven Clustering (scregclust)

The goal of scregclust is to cluster genes by regulatory programs. To do so, genes are clustered into modules which in turn are associated with regulators. The algorithm alternates between associating regulators to modules and reallocating target genes into modules.

• The documentation for this package can be found at https://scmethods.github.io/scregclust/
• A detailed description of the algorithm and an in-depth evaluation of its properties can be found in our original research article Larsson, Held, et al. (2024) Reconstructing the regulatory programs underlying the phenotypic plasticity of neural cancers. Nature Communications 15, 9699 DOI 10.1038/s41467-024-53954-3

Installation

You can install the stable version of scregclust from CRAN with

install.packages("scregclust")

You can install the current development version of scregclust from GitHub with:

# install.packages("devtools")
devtools::install_github("scmethods/scregclust")