# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "GRaNIE" in publications use:'
type: software
license: Artistic-2.0
title: 'GRaNIE: GRaNIE: Reconstruction cell type specific gene regulatory networks
  including enhancers using single-cell or bulk chromatin accessibility and RNA-seq
  data'
version: 1.9.3
abstract: Genetic variants associated with diseases often affect non-coding regions,
  thus likely having a regulatory role. To understand the effects of genetic variants
  in these regulatory regions, identifying genes that are modulated by specific regulatory
  elements (REs) is crucial. The effect of gene regulatory elements, such as enhancers,
  is often cell-type specific, likely because the combinations of transcription factors
  (TFs) that are regulating a given enhancer have cell-type specific activity. This
  TF activity can be quantified with existing tools such as diffTF and captures differences
  in binding of a TF in open chromatin regions. Collectively, this forms a gene regulatory
  network (GRN) with cell-type and data-specific TF-RE and RE-gene links. Here, we
  reconstruct such a GRN using single-cell or bulk RNAseq and open chromatin (e.g.,
  using ATACseq or ChIPseq for open chromatin marks) and optionally (Capture) Hi-C
  data. Our network contains different types of links, connecting TFs to regulatory
  elements, the latter of which is connected to genes in the vicinity or within the
  same chromatin domain (TAD). We use a statistical framework to assign empirical
  FDRs and weights to all links using a permutation-based approach.
authors:
- family-names: Arnold
  given-names: Christian
  email: chrarnold@web.de
- family-names: Zaugg
  given-names: Judith
  email: judith.zaugg@embl.de
- family-names: Moussa
  given-names: Rim
  email: rim.moussa01@gmail.com
repository: https://bioc.r-universe.dev
url: https://git.embl.de/grp-zaugg/GRaNIE
contact:
- family-names: Arnold
  given-names: Christian
  email: chrarnold@web.de
identifiers:
- type: url
  value: https://grp-zaugg.embl-community.io/GRaNIE