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# CITATION 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 "scCompoundDE" in publications use:'
type: software
license: MIT
title: 'scCompoundDE: Compositional and Transcriptional Decomposition of Pseudo-Bulk
  Differential Expression'
version: 0.99.0
abstract: 'scCompoundDE decomposes pseudo-bulk differential expression (DE) signals
  into two orthogonal components: transcriptional changes (cell-intrinsic expression
  shifts) and compositional changes (shifts in the relative abundance of cell subtypes).
  Standard pseudo-bulk DE tools confound these two sources of signal, producing spurious
  DE calls when subtype proportions differ between conditions. scCompoundDE fits per-subtype
  limma-voom models, estimates subtype proportion shifts, and uses a z-score-normalized
  decomposition to assign each gene a TC_ratio score — the fraction of its DE signal
  attributable to transcription versus composition. Genes are then classified as transcriptional
  (real biology), compositional (artifact), or mixed (requires caution). All functions
  operate natively on SingleCellExperiment objects and return a CDEResult S4 object
  that extends the standard DE output with full decomposition statistics.'
authors:
- family-names: Jana
  given-names: Subhadip
  email: subhadipjana1409@gmail.com
  orcid: https://orcid.org/0009-0003-7860-2853
repository: https://biocstaging.r-universe.dev
repository-code: https://github.com/SubhadipJana1409/scCompoundDE
commit: a791896402573dff5f4f056c9261871461980a0a
url: https://github.com/SubhadipJana1409/scCompoundDE
date-released: '2026-05-05'
contact:
- family-names: Jana
  given-names: Subhadip
  email: subhadipjana1409@gmail.com
  orcid: https://orcid.org/0009-0003-7860-2853