In this study, we evaluated various methods for differential expression analysis in single-cell transcriptomics, addressing challenges related to pseudoreplication. The tested methods include DESeq2, MAST, DREAM, scVI, Permutation Test, distinct, and t-test. Additionally, we adapted Hierarchical Bootstrapping for single-cell data analysis. Our focus was on benchmarking various scenarios and providing method recommendations for further single-cell differential expression analysis studies"
This repository contains a Nextflow pipeline used in the manuscript Single-cell Differential Expression Analysis Between Conditions Within Nested Settings. The pipeline reproduces all the results and figures presented in the manuscript.
Ensure you have the following software installed:
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Clone this repository to your local machine:
git clone https://github.com/LeonHafner/sc-guidelines.git cd sc-guidelines -
Execute the pipeline from the project's base directory:
nextflow run .
The figures generated by the pipeline can be found in the output directory specified in the configuration file (nextflow.config) or via the command line parameter --output (default is ./output).
The required software for the processes within the pipeline is provided in containerized environments using Docker containers. These containers are available on DockerHub and will be automatically fetched and executed by Nextflow using Apptainer.