NewWave：一个用于单细胞 RNA-seq 数据降维和批次效应去除的可扩展 R/Bioconductor 包。
NewWave: a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA-seq data.
机构信息
Department of Biology, Università degli Studi di Padova, Padova 35100, Italy.
Department of Statistical Science, Università degli studi di Padova, Padova 35100, Italy.
出版信息
Bioinformatics. 2022 Apr 28;38(9):2648-2650. doi: 10.1093/bioinformatics/btac149.
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.
摘要
我们提出了 NewWave，这是一个可扩展的 R / Bioconductor 包，用于单细胞 RNA 测序数据的降维和批次效应去除。为了实现可扩展性，NewWave 使用了小批量优化，并且可以处理内存外数据，使用户能够分析具有数百万个细胞的数据集。
可用性和实现
NewWave 作为一个开源 R 包实现，可通过 Bioconductor 项目在 https://bioconductor.org/packages/NewWave/ 获取。
补充信息
补充数据可在 Bioinformatics 在线获取。
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