/seurat-wrappers

Community-provided extensions to Seurat

Primary LanguageRGNU General Public License v3.0GPL-3.0

SeuratWrappers

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')

Method Listing

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/scran.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