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README.md
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 =================================================================================================================================================================================================================================================================== This project is currently under active development. # Repository structure This repository for our *GRaNIE* package (**G**ene **R**egul**a**tory **N**etwork **I**nference including **E**nhancers) ***GRaNIE* is soon included on *Bioconductor*. The package and installation instructions can be found here: [https://bioconductor.org/packages/GRaNIE](https://bioconductor.org/packages/GRaNIE)** In addition, the full documentation 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)** **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 # Bug Reports, Feature Requests and Contact Information Please check out **[the main page](https://grp-zaugg.embl-community.io/GRaNIE)** for how to get in contact with us.