genBaRcode

genBaRcode processes next-generation sequencing (NGS) reads to identify, quantify, and analyze artificial genetic barcodes for tracing clonal progeny.

Key Features:

• Flexibility in data handling: Processes NGS reads with varying barcode structures, accommodating both simple and complex designs.
• Barcode identification and quantification: Identifies artificial genetic sequences introduced into genomes and quantifies barcode abundance.
• Error-correction approaches: Implements multiple error-correction strategies to account for sequencing errors and improve identification accuracy.
• Visualization tools: Provides routines to visualize barcode similarities and other derived metrics for data interpretation.
• Standardization and reproducibility: Supports standardized analysis strategies to enable reproducible barcode data analysis across studies.

Scientific Applications:

• Lineage tracing: Traces clonal progeny to follow cellular lineage over time using genetic barcodes.
• Developmental biology: Enables tracking of cell fate and lineage dynamics in developmental studies.
• Cancer research: Facilitates analysis of clonal expansion and dynamics in tumor cell populations.

Methodology:

Implemented in R, the package processes NGS reads, performs sequence identification and quantification, applies multiple error-correction strategies, and generates visualization outputs.