# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "damidBind" in publications use:'
type: software
license: GPL-3.0-only
title: 'damidBind: Differential Binding and Expression Analysis for DamID-seq Data'
version: 1.1.0
doi: 10.32614/CRAN.package.damidBind
abstract: The damidBind package provides a straightforward formal analysis pipeline
  to analyse and explore differential DamID binding, gene transcription or chromatin
  accessibility between two conditions. The package imports processed data from DamID-seq
  experiments, either as external raw files in the form of binding bedGraphs and GFF/BED
  peak calls, or as internal lists of GRanges objects. After optionally normalising
  data, combining peaks across replicates and determining per-replicate peak occupancy,
  the package links bound loci to nearby genes. For RNA Polymerase DamID data, the
  package calculates occupancy over genes, and optionally calcualates the FDR of significantly-enriched
  gene occupancy. damidBind then uses either limma (for conventional log2 ratio DamID
  binding data) or NOIseq (for counts-based CATaDa chromatin accessibility data) to
  identify differentially-enriched regions, or differentially epxressed genes, between
  two conditions. The package provides a number of visualisation tools (volcano plots,
  Gene Ontology enrichment plots via ClusterProfiler and proportional Venn diagrams
  via BioVenn for downstream data exploration and analysis. An powerful, interactive
  IGV genome browser interface (powered by Shiny and igvShiny) allows users to rapidly
  and intuitively assess significant differentially-bound regions in their genomic
  context.
authors:
- family-names: Marshall
  given-names: Owen
  email: owen.marshall@utas.edu.au
  orcid: https://orcid.org/0000-0003-1605-3871
repository: https://bioc.r-universe.dev
repository-code: https://github.com/marshall-lab/damidBind
commit: 137db7ea256f7931296f3b1e87449a1f37fb7cbf
url: https://marshall-lab.org/damidBind
date-released: '2026-04-28'
contact:
- family-names: Marshall
  given-names: Owen
  email: owen.marshall@utas.edu.au
  orcid: https://orcid.org/0000-0003-1605-3871