NewWave: a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA-seq data

Abstract

Summary: We present NewWave, a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA sequencing data. To achieve scalability, NewWave uses mini-batch optimization and can work with out-of-memory data, enabling users to analyze datasets with millions of cells.

Availability and implementation: NewWave is implemented as an open-source R package available through the Bioconductor project at https://bioconductor.org/packages/NewWave/.

Supplementary information: Supplementary data are available at Bioinformatics online.