search

satijalab / seurat-wrappers

Community-provided extensions to Seurat
GNU General Public License v3.0
307 stars 131 forks source link
community single-cell-analysis single-cell-genomics

readme

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