A scalable R package for dimensionality reduction and batch effect removal of single-cell RNA-seq data.
NewWave is available on Bioconductor!
BiocManager::install("NewWave")
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.