BARtab and bartools

BARtab and bartools streamline the extraction, quality control, analysis, and visualization of lineage barcodes from population-level, single-cell, and spatial transcriptomics experiments.

Key Features:

• BARtab pipeline: A portable and scalable Nextflow pipeline for dataset pre-processing of cellular barcoding data.
• bartools R package: An open-source R package for downstream analysis and visualization of cellular barcoding datasets.
• Integrated workflow: Combined toolkit providing end-to-end cellular barcoding analysis from raw data to interpretable results.
• Multi-modal data support: Methods handle barcodes from population-level, single-cell, and spatial transcriptomics experiments.

Scientific Applications:

• Lineage tracing: Tracing of cell lineages across biological contexts by analyzing heritable synthetic barcodes coupled to high-throughput sequencing.
• Single-cell transcriptomics: Incorporation of lineage information into single-cell transcriptomics readouts for combined lineage and gene expression analysis.
• Spatial transcriptomics: Integration of cellular barcoding with spatial transcriptomics to map lineage relationships in tissue context.
• Bulk transcriptomics: Analysis of barcoding information from population-level sequencing experiments.

Methodology:

BARtab is implemented as a Nextflow pipeline; bartools is implemented as an R package. The integrated workflow performs barcode extraction, quality control, analysis, and visualization.