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README.md
In NewWave: Negative binomial model for scRNA-seq
NewWave
A scalable R package for dimensionality reduction and batch effect removal
of single-cell RNA-seq data.
How to install
Clone this repository on your machine and than install it
install.packages("path/to/NewWave", repos = NULL, type="source")
This package depends on SharedObject 1.3.15, it is a development version that can be found on Bioconductor-devel or on the github page linked below.
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 more deteiled case of use is shown in the vignette.
Useful links
Try the NewWave package in your browser
Any scripts or data that you put into this service are public.
NewWave documentation built on Dec. 26, 2020, 6 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
NewWave
A scalable R package for dimensionality reduction and batch effect removal of single-cell RNA-seq data.
How to install
Clone this repository on your machine and than install it
install.packages("path/to/NewWave", repos = NULL, type="source")
This package depends on SharedObject 1.3.15, it is a development version that can be found on Bioconductor-devel or on the github page linked below.
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 more deteiled case of use is shown in the vignette.
Useful links
Try the NewWave package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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