Gene Regulatory Network Inference including Enhancers: Reconstruction and evaluation of data-driven, cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNAseq data
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This project is currently under active development.
Repository structure
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This repository for our *GRaNIE* package (**G**ene **R**egul**a**tory **N**etwork **I**nference including **E**nhancers)
The full documentation for the all packages is available at the following stable URL and will soon be extended and completed:
**[https://grp-zaugg.embl-community.io/GRaNIE](https://grp-zaugg.embl-community.io/GRaNIE)**
**We are soon submitting our *GRaNIE* and the associated *GRaNIEData* for being included on *Bioconductor*. Once we are accepted and the package is included in the stable release of *Bioconductor*, we will update the installation guidelines in the documentation.**
**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