README.md

In chrarnold/GRaNIE: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data

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 (Gene Regulatory Network Inference including Enhancers)

GRaNIE is soon included on Bioconductor. The package and installation instructions can be found here: 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

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 for how to get in contact with us.

chrarnold/GRaNIE documentation built on April 28, 2022, 2:18 a.m.