Gene Regulatory Network Inference including Enhancers (GRaNIE): Reconstruction and evaluation of data-driven, cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNAseq data

This website features our GRaNIE (Gene Regulatory Network Inference including Enhancers) package. It is currently under active development.

GRaNIE is now included in Bioconductor. The package and installation instructions can be found here as well as in the quick start vignette.

If you use our packages, please use the following citation (we will update it once the paper has been officially published):

GRaNIE and GRaNPA: Inference and evaluation of enhancer-mediated gene regulatory networks applied to study macrophages. Aryan Kamal, Christian Arnold, Annique Claringbould, Rim Moussa, Neha Daga, Daria Nogina, Maksim Kholmatov, Nila Servaas, Sophia Mueller-Dott, Armando Reyes-Palomares, Giovanni Palla, Olga Sigalova, Daria Bunina, Caroline Pabst, Judith B. Zaugg. bioRxiv 2021.12.18.473290; doi: https://doi.org/10.1101/2021.12.18.473290