# SCArray – Large-scale single-cell RNA-seq data manipulation with GDS files

Dr. Xiuwen Zheng
Computational Genomics, Genomics Research Center, AbbVie

Aug, 2021

# Introduction

- Single-cell technology development
  - larger and larger numbers of cells assayed per experiment
  - the scalability leveraging on-disk data processing (avoid out of memory)
- Genomic Data Structure (GDS) files
  - an alternative to HDF5 & TileDB
  - hierarchical structure to store array-oriented data sets
  - compress & decompress data internally
  - out-of-memory data storage and manipulation in R
- SCArray
  - applies GDS to single-cell data manipulation & analysis
  - utilizes DelayedArray & SingleCellExperiment in BioC
  - reuse existing analysis packages efficiently (e.g., scater) via internal “seed-aware” functions

# Workflow & Data Structure

# Key Functions in SCArray

# Example: Small-size Dataset

# Example: Large-size Dataset (1.3M mouse brain cells)

# Discussion

- SCArray
  - under development
  - GDS as a file-based representation
    - a DelayedArray backend
    - for large-scale single-cell data storage & manipulation
  - leverage existing analysis R packages (e.g., scater)
    - via DelayedMatrix
- Plans
  - further integrate with Bioconductor infrastructure
    - GDSArray, DelayedMatrixStats, …
  - reimplement some memory-intensive algorithms

# Acknowledgements

- Genomics Research Center (GRC), AbbVie
  - Astrid Wachter
  - Priyanka Vijay
  - Yating(Claire) Chai
  - Zheng Zha
- Bioconductor
  - Qian Liu (Roswell Park Comprehensive Cancer Center)
- National Center for Supercomputing Applications (NCSA)
  - University of Illinois at Urbana-Champaign (UIUC)