Nikola de LANGE

Identification of cell-type and time point specific gene regulatory networks with DREMflow

The role of gene regulation during differentiation can be better understood if gene expression and
chromatin accessibility are observed jointly over time. Such time course regulatory analysis
eventually yields more detailed gene regulatory networks than expression data alone. Here, we
describe Dynamics Regulatory Events Miner Snakemake workflow (DREMflow) which combines
temporal RNA-seq and temporal ATAC-seq data to identify cell type and time point specific gene
regulatory networks. Using the workflow management system Snakemake and the package manager
Mamba we provide a multi-omics analysis pipeline that combines the necessary preprocessing for
the application of DREM with quality control measures and additional downstream analysis for the

inference of key transcription factors during differentiation. To ensure fluent execution and avoid
intermediate handling of data we replaced the java graphical user interface of DREM with
visualization in R allowing a continues analysis from raw reads to the final results. DREMflow enables
users to perform complex multi-omics analysis reproducibly with minimal setup and configuration.
Keywords: epigenetics, bioinformatics, multi-omics

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