# NewWave A scalable R package for dimensionality reduction and batch effect removal of single-cell RNA-seq data. ## How to install NewWave is available on Bioconductor! ``` BiocManager::install("NewWave") ``` ## How to use If you have your data stored in a SummarizedExperiment object with batch effect variable called "batch" stored in colData then: ``` newWave(data,X = "~batch") ``` In the X matrix you can teoretically store any variable related to the cell, both quantitative and qualitative. If you a batch variable, it must be a factor. A complete case of use is shown in the vignette. In the link to the workshop you can find a more detailed explanation plus an example of the usage with DelayedArray and HDF5 files. ## Useful links [EuroBioc2020 workshop](https://fedeago.github.io/SurfingNewWave/) [ZINB-WaVE article](https://www.nature.com/articles/s41467-017-02554-5) [ZINB-WaVE package](https://bioconductor.org/packages/release/bioc/html/zinbwave.html) [SharedObject package](https://github.com/Jiefei-Wang/SharedObject)