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

Federico Agostinis¹, Chiara Romualdi¹, Gabriele Sales¹

¹Department of Biology, Università degli Studi di Padova, Padova 35100, Italy.

Bioinformatics (Oxford, England)

|March 10, 2022

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.

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