bartools

Tools for the analysis of cellular barcoding datasets

Introduction

Cellular barcoding is a powerful and widespread method to accurately track the progeny of a clone within a population of cells, enabling the dissection of biological phenomena at single cell resolution. However there remains a need for scalable and standardised open-source tools to pre-process and visualise cellular barcoding datasets. The bartools package is an R-based toolkit for the analysis of cellular barcoding information from high throughput sequencing datasets. The package consists of a suite of functions to annotate, analyse and plot DNA barcodes that are read out using common high throughput sequencing methodologies such as from Illumina machines. The bartools package is optimised for use with SPLINTR lineage barcode libraries however the functions within can be adapted to any cellular barcoding methodology that utiilses random DNA barcodes.

Installation

You can install bartools from GitHub:

# first install Bioconductor dependencies
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(c("edgeR", "limma", "ComplexHeatmap"))

# then install bartools via GitHub
if (!requireNamespace("devtools", quietly = TRUE)) {
  install.packages("devtools")
}
devtools::install_github("DaneVass/bartools", dependencies = TRUE, force = TRUE)

Getting started

See vignette(bartools) for more details and usage examples.

Documentation

See the Docs for full package documentation.

For bulk level analysis see the quickstart vignette
For single cell data preprocessing and import see the import_qc_single_cell vignette
For single cell data analysis see the single_cell_analysis vignette

Looking for a dataset preprocessing pipeline?

We have also developed BARtab, a pre-processing pipeline to automate the extraction and enumeration of barcode reads from raw sequence files. See the github for

Contact

The bartools package was developed by Dane Vassiliadis and Henrietta Holze. Please post any issues at https://github.com/DaneVass/bartools/issues