NewWave

'NewWave' is an R package for dimensionality reduction and batch effect removal in single-cell RNA sequencing data. It employs scalable methods, particularly mini-batch optimization, making it suitable for large datasets with millions of cells. The open-source package provides a scalable solution for analyzing single-cell RNA sequencing data, ensuring efficient dimensionality reduction and batch effect removal. The 'NewWave' package aims to enhance the analysis of extensive single-cell datasets, improving scalability and facilitating downstream analyses.

Topic

RNA-Seq;Transcriptomics;RNA

Detail

  • Operation: Dimensionality reduction;Regression analysis;Essential dynamics

  • Software interface: Library

  • Language: R

  • License: The GNU General Public License v3.0

  • Cost: Free

  • Version name: 1.12.0

  • Credit: The AIRC Foundation for Cancer Research in Italy, the National Cancer Institute of the National Institutes of Health, the Chan Zuckerberg Initiative DAF an advised fund of 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’.

  • Input: -

  • Output: -

  • Contact: Federico Agostinis federico.agostinis@outlook.com

  • Collection: -

  • Maturity: Stable

Publications

  • NewWave: a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA-seq data
  • Agostinis F, Romualdi C, Sales G, Risso D. NewWave: a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA-seq data. Bioinformatics. 2022 Apr 28;38(9):2648-2650. doi: 10.1093/bioinformatics/btac149. PMID: 35266509; PMCID: PMC9048694.
  • https://doi.org/10.1101/2021.08.02.453487
  • PMID: 35266509
  • PMC: PMC9048694

Download and documentation

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