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README.md
<img src="man/figures/logo.png" align="right" width="250"/> ## GRaNIE: Reconstruction and evaluation of data-driven, cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNAseq data This project is under active development. ### Repository structure This repository is for our *GRaNIE* package (**G**ene **R**egul**a**tory **N**etwork **I**nference including **E**nhancers). The accompanying [website](https://grp-zaugg.embl-community.io/GRaNIE) is **not** part of Bioconductor and independently build and maintained based on the development version of *GRaNIE*, which is hosted [in this repository](https://git.embl.de/grp-zaugg/GRaNIE). It may therefore differ from the *release version* of the package. For the *GRaNPA* package, see [here](https://grp-zaugg.embl-community.io/GRaNPA). ### Installation and Documentation ***GRaNIE* is now 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 for the development version is available at **[https://grp-zaugg.embl-community.io/GRaNIE](https://grp-zaugg.embl-community.io/GRaNIE)** and regularly updated and extended. ### Citation **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 For issues, bugs, and feature request, please see the [Issue Tracker](https://git.embl.de/grp-zaugg/GRaNIE/issues). If you have other questions or comments, feel free to contact us. We will be happy to answer any questions related to this project as well as questions related to the software implementation. For method-related questions, contact Judith B. Zaugg (judith.zaugg@embl.de). For technical questions, contact Christian Arnold (christian.arnold@embl.de). We will aim to respond in a timely manner.