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scDAPP: a comprehensive single-cell transcriptomics analysis pipeline optimized for cross-group comparison.

Alexander Ferrena1,2, Xiang Yu Zheng1, Kevyn Jackson1

  • 1Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.

NAR Genomics and Bioinformatics
|September 30, 2024
PubMed
Summary

The single-cell Differential Analysis and Processing Pipeline (scDAPP) automates complex single-cell RNA sequencing data analysis. This R-based workflow enhances efficiency and transparency for comparative transcriptomic studies.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Single-cell transcriptomics is crucial for understanding cellular heterogeneity and condition-specific gene expression.
  • Analyzing large, complex single-cell datasets requires advanced, standardized bioinformatics approaches.
  • Existing analytical methods for single-cell RNA sequencing (scRNA-seq) data are diverse and evolving.

Purpose of the Study:

  • To develop an automated, efficient, and flexible R-based pipeline for comparative analysis of single-cell transcriptomic data.
  • To standardize the processing and analysis of scRNA-seq data across multiple groups or conditions.
  • To facilitate seamless transition from raw data to biological interpretation for researchers.

Main Methods:

  • Developed the single-cell Differential Analysis and Processing Pipeline (scDAPP) as an R-based workflow.
  • Automated pre-processing steps using data-learnt parameters and integrated previously benchmarked software.
  • Enabled comparative analysis at both single-cell and pseudobulking levels for transcriptomic data.

Main Results:

  • scDAPP automates complex comparative analyses of single-cell transcriptomic data.
  • The pipeline generates comprehensive intermediate and final results with extensive data visualization.
  • Enhanced transparency in computational analysis and parameter choices for scRNA-seq studies.

Conclusions:

  • scDAPP provides a valuable, user-friendly tool for both novice and expert scRNA-seq researchers.
  • The pipeline streamlines the analysis of cross-group differences in cell populations and gene expression.
  • Freely available on GitHub, scDAPP promotes reproducible and accessible single-cell data analysis.