In addition to the core Seurat package, we recommend installing several other packages that enhance the functionality and utility of Seurat. A brief description of each is listed below with links to more complete documentation.
SeuratData
SeuratData is an R package that distributes example datasets in the form of Seurat objects using R’s internal package and data management systems. We use it to provide easy access to datasets that are used in the Seurat vignettes.
BPCells
- Website: https://bnprks.github.io/BPCells/
- GitHub: https://github.com/bnprks/BPCells
BPCells is an R package that allows for computationally efficient single-cell analysis. It utilizes bit-packing compression to store counts matrices on disk and C++ code to cache operations.
RNA Fingerprinting
RNA Fingerprinting is an R package that maps transcriptional responses in scRNA-seq experiments to perturbation dictionaries. Users can estimate fingerprints of reference perturbations and map new queries at the level of individual cells or groups of cells.
AzimuthAPI
AzimuthAPI is an R package that provides an interface to the Pan-human Azimuth neural network for cell type annotation of single-cell and spatial transcriptomics data. Users can run annotation through a cloud-based API or locally in R.
Signac
- Website: https://stuartlab.org/signac/
- GitHub: https://github.com/stuart-lab/signac
Signac is an R toolkit for the analysis, interpretation, and exploration of single-cell chromatin datasets, including the following features:
- Calculating single-cell QC metrics
- Dimensional reduction, visualization, and clustering
- Identifying cell type-specific peaks
- Visualizing ‘pseudo-bulk’ coverage tracks
- Integration with single-cell RNA-seq datasets
presto
Presto is an R package that performs a fast Wilcoxon rank sum test and auROC analysis, which Seurat uses in the differential expression workflow.