This project analyses scRNA-Seq data from hepatocellular carcinoma using the EcoTyper software by Steen/Luca et al. (2021). This repository contains scripts used for data analysis and environment setup.
This project aims to assess the uses of EcoTyper for scRNA-seq from Hepatcarcinoma samples. We are going to analyse scRNA-seq (15 cancer, 2 normal) liver biopsies to identify the different ecotypes in there.
First, set up the environment using the setup/setup_environment.sh script. Once finished, activate the environment using conda activate EcoTyper (or whatever name you passed to the script as optional argument).
Ecotyper requires TSV-formatted CPM or TPM input data not containing spaces or dashes in the sample names. Hence, some pre-processing may be necessary. The environment installs the package eco_helper which can be used to pre-process the data.
EcoTyper can be run by adjusting the configuration files in scripts/experiments/ecotyper and by then running the script scripts/experiments/ecotyper/scRNAseq_discovery.slurm.
eco_helper can be used to automatically perform gene set enrichment analysis (GSEA) on the produced ecotypes. Output formats are raw files, a jupyter notebook (requiring an additional configuration file in yaml format), and/or a pickle file. The pickle file can be loaded into the eco_helper Viewer web-app to explore GSEA results more easily.