ArticleCell reports methods2024
Analysis of synthetic cellular barcodes in the genome and transcriptome with BARtab and bartools.
Article in Cell reports methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Φ-Space ST: A platform-agnostic method to identify cell states in spatial transcriptomics studies.Cell reports methods · 2026Article
- Charting single-cell lineages with synthetic and natural barcodes.Nature reviews. Genetics · 2026Review
- barbieQ: an R software package for analysing barcode count data from clonal tracking experiments.Bioinformatics (Oxford, England) · 2026Article
- Antigen reactivity defines tissue-resident memory and exhausted T cells in tumors.Nature immunology · 2026Article
- QuiCAT: a scalable and flexible framework for mapping synthetic sequences.Bioinformatics (Oxford, England) · 2025Article
- Catalytic Inhibition of KAT6/KAT7 Enhances the Efficacy and Overcomes Primary and Acquired Resistance to Menin Inhibitors in MLL Leukemia.Cancer discovery · 2025Article
- Single-Cell Lineage Tracing and Clonal State-Fate Analysis.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Synthetic DNA barcodes identify singlets in scRNA-seq datasets and evaluate doublet algorithms.Cell genomics · 2024Article
- A computational tool suite to facilitate single-cell lineage tracing analyses.Cell reports methods · 2024Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cellular barcoding is a lineage-tracing methodology that couples heritable synthetic barcodes to high-throughput sequencing, enabling the accurate tracing of cell lineages across a range of biological contexts. Recent studies have extended these methods by incorporating lineage information into single-cell or spatial transcriptomics readouts. Leveraging the rich biological information within these datasets requires dedicated computational tools for dataset pre-processing and analysis. Here, we present BARtab, a portable and scalable Nextflow pipeline, and bartools, an open-source R package, designed to provide an integrated end-to-end cellular barcoding analysis toolkit. BARtab and bartools contain methods to simplify the extraction, quality control, analysis, and visualization of lineage barcodes from population-level, single-cell, and spatial transcriptomics experiments. We showcase the utility of our integrated BARtab and bartools workflow via the analysis of exemplar bulk, single-cell, and spatial transcriptomics experiments containing cellular barcoding information.
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