@@ -5,18 +5,21 @@ This project is currently under active development.
Repository structure
----------------------
This repository for our *GRaNIE* packages (**G**ene **R**egul**a**tory **N**etwork **I**nference including **E**nhancers) currently contains everything that is related to this project and is organized into the following 3 packages:
-<code>GRaNIE</code> (stable version)
-<code>GRaNIEdev</code> (development version, use with care and only if you need access to the newest set of features)
This repository for our `GRaNIE` packages (**G**ene **R**egul**a**tory **N**etwork **I**nference including **E**nhancers) currently contains everything that is related to this project and is organized into the following 3 packages:
-<code>GRaNIE</code>
-<code>GRaNIEdata</code> (example dataset that the Vignette uses)
The full documentation for the all packages is available at the following stable URL and will soon be extended and completed:
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
**Please use the following citation:**
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
