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Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
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barbieQ: an R software package for analysing barcode count data from clonal tracking experiments.

Liyang Fei1,2, Jovana Maksimovic1,2, Alicia Oshlack1,2

  • 1Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.

Bioinformatics (Oxford, England)
|June 16, 2026
PubMed
Summary
This summary is machine-generated.

A new R package, barbieQ, offers a generalized workflow for analyzing DNA barcode count data from single-cell lineage tracing experiments. It provides robust statistical tests and quality control to improve clonal tracking analysis across diverse samples.

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Area of Science:

  • * Computational Biology
  • * Genomics
  • * Bioinformatics

Background:

  • * Single-cell lineage tracing utilizes DNA barcodes to track cell populations and their progeny.
  • * Current analysis of barcode count data lacks a standardized, robust workflow, often relying on bespoke methods.
  • * A generalized approach is needed for preprocessing and statistical analysis of barcode count data.

Purpose of the Study:

  • * To introduce barbieQ, a Bioconductor R package for analyzing barcode count data.
  • * To provide data-driven quality control, filtering, and visualization tools.
  • * To implement robust statistical tests for differential barcode analysis.

Main Methods:

  • * Development of the barbieQ R package available on Bioconductor.
  • * Implementation of two statistical tests: differential barcode proportion and differential barcode occurrence.
  • * Utilizing regression models to handle complex experimental designs and account for sample variability.

Main Results:

  • * barbieQ offers data-driven quality control and filtering capabilities.
  • * The package includes extensive visualizations for barcode count data.
  • * Validated statistical tests demonstrate appropriate statistical properties (size and power) and outperform existing methods.

Conclusions:

  • * barbieQ provides a generalized and robust workflow for analyzing single-cell lineage tracing barcode data.
  • * The package enhances the statistical rigor and analytical power for clonal tracking studies.
  • * barbieQ facilitates more reliable comparisons of clonal composition across different experimental groups.