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cff-version: 1.2.0
message: 'To cite package "barmixR" in publications use:'
type: software
license: GPL-3.0-only
title: 'barmixR: Bayesian Modeling of Barcoded Tumor Mixtures for Quantitative Treatment
  Resistance Analysis'
version: 0.99.2
abstract: Implements the Bayesian modeling framework underlying the barmixR (BARcode
  MIXture analysis) platform for high-throughput quantitative analysis of genotype-specific
  treatment responses in pooled cancer cell populations. The package integrates barcode
  sequencing count data with volumetric measurements such as tumor volume (in vivo)
  or cellular confluency (in vitro) using hierarchical probabilistic models. Barcode
  counts are modeled with a Dirichlet–multinomial distribution to account for compositional
  sequencing data, while volumetric measurements are modeled using log-normal (tumor
  volume) or beta (confluency) likelihoods. Posterior inference is performed using
  Hamiltonian Monte Carlo through 'rstan'. The resulting posterior distributions enable
  estimation of clone-specific quantitative treatment resistance (QTR) together with
  uncertainty propagation from both sequencing and volumetric data. Additional functions
  provide posterior predictive checks, estimation of resistance ratios, treatment
  ranking, and visualization of resistance landscapes using violin plots and bubble
  heatmaps. The methods are designed for multiplexed lineage-tracing experiments in
  cancer research and were developed to analyze treatment resistance in gastrointestinal
  stromal tumors (GIST), but are broadly applicable to barcoding-based studies of
  treatment response and clonal dynamics across diverse cancer types.
authors:
- family-names: Darbalaei
  given-names: Mohammad
  email: mohammad.darbalaei@uni-due.de
  orcid: https://orcid.org/0009-0003-4561-0048
- family-names: Hoffmann
  given-names: Daniel
  orcid: https://orcid.org/0000-0003-2973-7869
repository: https://bioc.r-universe.dev
repository-code: https://github.com/MohammadDarbalaei/barmixR
commit: 1509ed7e005f7de0cd6fdb50f7e290a4f903ea2d
url: https://github.com/MohammadDarbalaei/barmixR
date-released: '2026-06-27'
contact:
- family-names: Darbalaei
  given-names: Mohammad
  email: mohammad.darbalaei@uni-due.de
  orcid: https://orcid.org/0009-0003-4561-0048