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# CITATION.cff file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "DgeaHeatmap" in publications use:'
type: software
license: GPL-3.0-only
title: 'DgeaHeatmap: Implementation of Functions to Analyze Nanostring and Other Data
  for DGE and to Generate Heatmaps'
version: 0.99.0
doi: 10.1093/bioadv/vbaf194
abstract: Package for data extraction from Nanostring GeoMx DSP data, also works for
  other data. Simple functions for Differential Expression Analysis. User-friendly
  and highly customizable functions for heatmap generation.
authors:
- family-names: Lancelle
  given-names: Leonie Johanna
  email: leonie.lancelle@uni-bielefeld.de
  orcid: https://orcid.org/0009-0004-3138-0752
preferred-citation:
  type: article
  title: 'DgeaHeatmap: an R package for transcriptomic analysis and heatmap generation'
  authors:
  - family-names: Lancelle
    given-names: Leonie J
  - family-names: Potru
    given-names: Phani S
  - family-names: Spittau
    given-names: Bjoern
  - family-names: Wiemann
    given-names: Susanne
  journal: Bioinformatics Advances
  volume: '5'
  issue: '1'
  year: '2025'
  month: '8'
  issn: 2635-0041
  abstract: The growing use of transcriptomic data from platforms like Nanostring
    GeoMx DSP demands accessible and flexible tools for differential gene expression
    analysis and heatmap generation. Current web-based tools often lack transparency,
    modifiability, and independence from external servers creating barriers for researchers
    seeking customizable workflows, as well as data privacy and security. Additionally,
    tools that can be utilized by individuals with minimal bioinformatics expertise
    provide an inclusive solution, empowering a broader range of users to analyze
    complex data effectively.Here, we introduce Differential Gene Expression Analysis
    and Heatmaps (DgeaHeatmap), an R package offering streamlined and user-friendly
    functions for transcriptomic data analysis particularly yielded by Nanostring
    GeoMx DSP instruments. The package supports both normalized and raw count data,
    providing tools to preprocess, filter, and annotate datasets. DgeaHeatmap leverages
    Z-score scaling and k-means clustering for customizable heatmap generation and
    incorporates a workflow adapted from GeoMxTools for handling raw Nanostring GeoMx
    DSP data. By enabling server-independent analyses, the package enhances flexibility,
    transparency, and reproducibility in transcriptomic research.The package DgeaHeatmap
    is freely available on GitLab (https://gitlab.ub.uni-bielefeld.de/spittaulab/Dgea/Heatmap/Package.git).
  doi: 10.1093/bioadv/vbaf194
  url: https://doi.org/10.1093/bioadv/vbaf194
  start: vbaf194
repository: https://biocstaging.r-universe.dev
commit: 65a509be682ef287f8d7158d8a9555e8ad95e845
url: https://gitlab.ub.uni-bielefeld.de/spittaulab/Dgea_Heatmap_Package
date-released: '2026-07-20'
contact:
- family-names: Lancelle
  given-names: Leonie Johanna
  email: leonie.lancelle@uni-bielefeld.de
  orcid: https://orcid.org/0009-0004-3138-0752