compact: co-expression module perturbation analysis

compact is a framework for performing CO-expression Module Perturbation Analysis in Cellular Transcriptomes. Building off of our previous method hdWGCNA, compact applies direct perturbations to co-expression network hub genes, and uses the network structure to propagate the perturbation signal to other linked genes in the network. This framework is highly flexible to perform knock-in, knock-down, or knock-out perturbations on different networks and sets of genes and in different cell lineages, allowing researchers to explore a wide range of strategies mimicking various experimental conditions and interventions.

compact is under active development, and is currently an alpha version. This means that many features of the final package are missing, and current features are subject to change throughout development. The first major release of compact will coincide with our forthcoming publication.

To get started, please install the package and then visit the co-expression module perturbation analysis tutorial.

Installation

We recommend creating an R conda environment environment for compact.

conda create -n compact -c conda-forge r-base r-essentials
conda activate compact

Install the required packages in R

# install BiocManager
install.packages("BiocManager")
BiocManager::install()

# install latest version of Seurat from CRAN
install.packages("Seurat")

# install devtools
BiocManager::install("devtools")

# install hdWGCNA, velocyto.R, and compact from devtools
devtools::install_github('smorabit/hdWGCNA', ref='dev')
devtools::install_github("velocyto-team/velocyto.R")
devtools::install_github('smorabit/compact')