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Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

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Single cell lineage reconstruction using distance-based algorithms and the R package, DCLEAR.

Wuming Gong¹, Hyunwoo J Kim², Daniel J Garry¹

¹Lillehei Heart Institute, University of Minnesota, Minneapolis, USA.

BMC Bioinformatics

|March 25, 2022

Summary

DCLEAR, a new R package, enhances single-cell lineage reconstruction using advanced CRISPR gene editing data. It introduces novel distance estimation methods, outperforming traditional approaches for accurate cell lineage tree prediction.

Keywords:

Cell lineage tracing Lineage reconstruction Machine learning Simulation

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Published on: May 8, 2020

Area of Science:

Computational Biology
Genomics
Bioinformatics

Background:

CRISPR gene editing enables cell lineage tree prediction via edited barcodes.
Assessing the performance of existing cell lineage reconstruction methods is crucial.
The Cell Lineage Reconstruction Dream Challenge (2020) spurred advancements in the field.

Purpose of the Study:

To develop and present the DCLEAR R package for single-cell lineage reconstruction.
To introduce novel methods for distance matrix estimation in lineage reconstruction.
To evaluate the performance of new distance methods against traditional ones.

Main Methods:

DCLEAR employs a two-step approach: distance matrix estimation and tree reconstruction.
Two novel methods for distance matrix estimation were developed and implemented in DCLEAR.
The R package contains the code for these methods, submitted to a challenge competition.

Main Results:

The novel distance estimation methods in DCLEAR significantly improve performance over the Hamming distance.
DCLEAR's methods were validated through participation in the Cell Lineage Reconstruction Dream Challenge, winning two sub-challenges.
The package provides open-source R code for reproducible research.

Conclusions:

DCLEAR offers a powerful and effective resource for single-cell lineage reconstruction.
The package facilitates accurate cell lineage tree prediction using advanced computational methods.
DCLEAR is freely available, promoting wider adoption and research in the field.