This repository is aimed at reproducing the results of the paper "Network analysis of hepatocellular carcinoma liquid biopsies augmented by single-cell sequencing data". Front. Genet. 13:921195. The code is written in R.
For full reproducibility, users are advised to first create a conda environment (How to install Miniconda) with the command conda env create --name cfwgcna_hcc --file cfwgcna_hcc.yml. This will install the necessary tools with the appropriate versions. As some tools were used in the original study with different versions, here the newer versions of said tools will be installed. Afterwards, the newly created conda environment can be activated with the command conda activate cfwgcna_hcc and the snakemake pipeline to reproduce the results can be run via snakemake -s snakemake_pipeline --cores X where "X" is the number of cores one wishes to use. Finally, the figures created with the software "Cytoscape" are not reproduced here and are made already available but if the user desires the figures can be recreated using the files in the "cfrna/results/modules/" directory.
The pipeline has been tested on a Linux system. Using 15 cores the full implementation of the pipeline takes approximately 12 hours.
For any questions, please contact [email protected]