SCUBA (Single Cell Unified Back end API) is a unified data accession interface for single-cell object classes. The package streamlines R data analysis for Seurat, SingleCellExperiment, and anndata objects by providing a consistent interface for data access, exploration, and visualization.
SCUBA relies on the reticulate package to operate on AnnData objects. Please make sure you follow the instructions on the reticulate page before moving on.
It is recommended to use conda environments to manage your python version that is being used by reticulate. A conda environment can be used on the current R session by using reticulate::use_condaenv(). If you want to make it automatically load on startup you can select your conda environment in RStudio > Options > Python.
You must have the following packages installed and available in your Python environment:
- Numpy
- Scipy
- Pandas
- AnnData
Run the command below to install SCUBA. BiocManager is used to automatically install Bioconductor dependencies (SCUBA is not a Bioconductor package).
If you plan to use SCUBA with anndata objects, use dependencies = TRUE. If you only plan to use SCUBA with Seurat and SingleCellExperiment objects, use dependencies = FALSE.
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# Set dependencies to FALSE if you do not plan to use anndata objects
BiocManager::install("amc-heme/SCUBA", dependencies = TRUE)
Please see our website for a user guide and more information.
Showers,W.M., Desai,J., Engel,K.L., Smith,C., Jordan,C.T. and Gillen,A.E. (2024) SCUBA implements a storage format-agnostic API for single-cell data access in R. 10.12688/f1000research.154675.1.
If any issues arise please file a Github issue on this repository.
