README.md

In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object

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 |

satijalab/seurat-wrappers documentation built on April 10, 2024, 3:25 p.m.