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 remotes

remotes::install_github('satijalab/seurat-wrappers')

Method Listing

Package	Vignette	Reference	Source
Monocle 3	Calculating Trajectories with Monocle 3 and Seurat	Cao et al, Nature 2019	https://cole-trapnell-lab.github.io/monocle3
scVelo	Estimating RNA Velocity using Seurat and scVelo	Bergen et al, bioRxiv 2019	https://scvelo.readthedocs.io
CoGAPS	Running CoGAPS on Seurat Objects	Stein-O’Brien et al, Cell Systems 2019	https://www.bioconductor.org/packages/release/bioc/html/CoGAPS.html
glmpca	Running GLM-PCA on a Seurat Object	Townes et al, Genome Biology 2019	https://github.com/willtownes/glmpca
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
alevin	Import alevin counts into Seurat	Srivastava et. al., Genome Biology 2019	https://github.com/k3yavi/alevin-Rtools
Nebulosa	Visualization of gene expression with Nebulosa	Jose Alquicira-Hernandez and Joseph E. Powell, Under Review	https://github.com/powellgenomicslab/Nebulosa
CIPR	Using CIPR with human PBMC data	Ekiz et. al., BMC Bioinformatics 2020	https://github.com/atakanekiz/CIPR-Package
miQC	Running miQC on Seurat objects	Hippen et. al., bioRxiv 2021	https://github.com/greenelab/miQC
tricycle	Running estimate_cycle_position from tricycle on Seurat Objects	Zheng et. al., bioRxiv 2021	https://www.bioconductor.org/packages/release/bioc/html/tricycle.html
PaCMAP	Running PaCMAP on Seurat Objects	Wang et. al, JMLR 2021; Huang et. al, Communications Biology 2022	https://github.com/YingfanWang/PaCMAP