<i>NewWave</i>: a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA-seq data-Reference-Cited by-同舟云学术

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

Published:2022-03-10 Issue:9 Volume:38 Page:2648-2650
ISSN:1367-4803
Container-title:Bioinformatics
language:en
Short-container-title:

Author:

Agostinis Federico¹^ORCID,Romualdi Chiara¹^ORCID,Sales Gabriele¹,Risso Davide²^ORCID

Affiliation:

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

2. Department of Statistical Science, Università degli studi di Padova , Padova 35100, Italy

Abstract

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.

Funder

AIRC Foundation for Cancer Research in Italy [AIRC

National Cancer Institute of the National Institutes of Health

Chan Zuckerberg Initiative DAF

Silicon Valley Community Foundation and by University of Padova Strategic Research Infrastructure Grant 2017

CAPRI: Calcolo ad Alte Prestazioni per la Ricerca e l’Innovazione

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

Link

https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btac149/42974083/btac149.pdf

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