SeuratWrappers is a collection of community-provided methods and extensions for Seurat, curated by the Satija Lab at NYGC. These methods comprise functionality not presently found in Seurat, and are able to be updated much more frequently.
Please see our contribution guide for assistance and guidelines in developing and adding new methods to SeuratWrappers
Individual method vignettes can be found in the docs/ directory, we recommend looking at the standard markdown (*.md) files when viewing on GitHub
Installation can be accomplished through devtools
devtools::install_github('satijalab/seurat-wrappers')| Package | Vignette | Reference | Source |
|---|---|---|---|
| Conos | Integration of datasets using Conos | Barkas et al, Nature Methods 2019 | https://github.com/hms-dbmi/conos |
| LIGER | Integrating Seurat objects using LIGER | Welch et al, Cell 2019 | https://github.com/MacoskoLab/liger |
| fastMNN | Running fastMNN on Seurat Objects | Nature Biotechnology 2018 | https://bioconductor.org/packages/release/bioc/html/batchelor.html |
| Harmony | Integration of datasets using Harmony | Korsunsky et al, bioRxiv 2018 | https://github.com/immunogenomics/harmony |
| ALRA | Zero-preserving imputation with ALRA | Linderman et al, bioRxiv 2018 | https://github.com/KlugerLab/ALRA |
| Velocity | Estimating RNA Velocity using Seurat | La Manno et al, Nature 2018 | https://velocyto.org |
| schex | Using schex with Seurat | Freytag, R package 2019 | https://github.com/SaskiaFreytag/schex |