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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 "cascadeR" in publications use:'
type: software
license: MIT
title: 'cascadeR: Shiny App to Explore Single-Cell Analysis'
version: 0.99.0
abstract: Interactive and modular shiny app for single-cell and spatial transcriptomic
  data exploration and management. Visualize cell clusters or groups using interactive
  cell embeddings, e.g. UMAP or t-SNE, or spatial views. Explore cell composition
  and quality control metrics using the metadata viewer module. Investigate the effect
  of clustering resolutions or compare annotation sources using cluster tree. Visualize
  gene expression using cell embeddings or in spatial context with feature plots and
  coexpression plots or in cell clusters using dotplots, violin plots. Manage marker
  tables from single-cell or pseudo-bulk analyses and track genes of interest using
  the gene scratchpad. Choose interesting cells with lasso selection directly from
  interactive plots and export for downstream analysis. Slice and dice datasets with
  custom filters based on cell metadata, gene expression or lasso selections. Efficiently
  handle large datasets using custom downsampling controls. CascadeR has cross-ecosystem
  compatibility with support for Seurat, SingleCellExperiment and AnnData objects.
  In addition, the app includes an integrated platform to manage multiple projects
  and user access that can be run on a central server to share with collaborators.
authors:
- family-names: Mitra
  given-names: Apratim
  email: apratim.mitra@gmail.com
  orcid: https://orcid.org/0000-0003-3279-0054
repository: https://biocstaging.r-universe.dev
repository-code: https://github.com/NICHD-BSPC/cascadeR
commit: 3c944e1f7344b998eb09c0419f7bc952ec862347
url: https://nichd-bspc.github.io/cascadeR/
date-released: '2026-09-18'
contact:
- family-names: Mitra
  given-names: Apratim
  email: apratim.mitra@gmail.com
  orcid: https://orcid.org/0000-0003-3279-0054