Package index • barbac

Core clustering

Abundance-ranked greedy Levenshtein clustering with a bit-parallel C++ kernel.

super_cluster2(): Fast Centroid-Based Sequence Clustering

Time-series visualisation

Stacked-area plots of lineage frequencies over time.

barbac_ts_area(): Stacked-area plot of barcode lineage frequencies over time
theme_barbac(): A publication-ready ggplot2 theme for barbac plots

Barcode extraction

barbac_xtr(): Extract Barcodes from BAM File
barbac_xtr.stats(): Generate Summary Statistics and Plots for Extracted Barcodes

QC and diagnostics

Quick-look summaries and plots for sanity-checking each stage of the pipeline.

plot_bam_stats(): Per-sample bar plot of mapping counts
cluster_stats(): Post-clustering QC summary

End-to-end pipeline orchestrator

run_cli_pipeline(): Run Full Barbac CLI Pipeline

Individual pipeline steps

Wrappers around FastQC, PEAR, minimap2 and samtools.

run_fastqc(): Run FastQC on all FASTQ files listed in a samples.csv file
run_multiqc(): Run MultiQC to summarize FastQC reports
run_pear_merge(): Merge paired-end reads using PEAR
run_minimap2(): Map merged reads to reference using minimap2 and process with samtools
summarise_bam_stats(): Summarise mapped and unmapped read counts from sorted BAM files

Environment management

Provision and activate a conda environment with the CLI tools.

configure_environment(): Configure Conda Environment for barbac
use_barbac_env(): Use barbac conda environment in the current R session
check_barbac_tools(): Check availability of tools in barbac conda environment

Package overview

barbac-package barbac: barbac: End-to-end DNA barcode lineage analysis