# seurat-wrappers

**Repository Path**: joyeric_admin_admin/seurat-wrappers

## Basic Information

- **Project Name**: seurat-wrappers
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: GPL-3.0
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2023-12-30
- **Last Updated**: 2024-07-29

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# SeuratWrappers

SeuratWrappers is a collection of community-provided methods and extensions for [Seurat](https://satijalab.org/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](https://github.com/satijalab/seurat.wrappers/wiki) for assistance and guidelines in developing and adding new methods to SeuratWrappers

Individual method vignettes can be found in the [`docs/`](https://github.com/satijalab/seurat.wrappers/tree/master/docs) directory, we recommend looking at the standard markdown (`*.md`) files when viewing on GitHub

Installation can be accomplished through [remotes](https://cran.r-project.org/package=remotes)

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

## Method Listing

| Package | Vignette | Reference | Source |
| ------- | -------- | --------- | ------ |
| Monocle 3 | [Calculating Trajectories with Monocle 3 and Seurat](http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/monocle3.html) | Cao et al, Nature 2019 | https://cole-trapnell-lab.github.io/monocle3 |
| scVelo | [Estimating RNA Velocity using Seurat and scVelo](http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/scvelo.html) | Bergen et al, bioRxiv 2019 | https://scvelo.readthedocs.io |
| CoGAPS  | [Running CoGAPS on Seurat Objects](http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/cogaps.html) | 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](http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/glmpca.html) | Townes et al, Genome Biology 2019 | https://github.com/willtownes/glmpca |
| Conos | [Integration of datasets using Conos](http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/conos.html) | Barkas et al, Nature Methods 2019 | https://github.com/hms-dbmi/conos |
| LIGER | [Integrating Seurat objects using LIGER](http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/liger.html) | Welch et al, Cell 2019 | https://github.com/MacoskoLab/liger |
| fastMNN | [Running fastMNN on Seurat Objects](http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/fast_mnn.html) | Nature Biotechnology 2018 | https://bioconductor.org/packages/release/bioc/html/batchelor.html |
| Harmony | [Integration of datasets using Harmony](http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/harmony.html) | Korsunsky et al, bioRxiv 2018 | https://github.com/immunogenomics/harmony |
| ALRA | [Zero-preserving imputation with ALRA](http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/alra.html) | Linderman et al, bioRxiv 2018 | https://github.com/KlugerLab/ALRA |
| Velocity | [Estimating RNA Velocity using Seurat](http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/velocity.html) | La Manno et al, Nature 2018 | https://velocyto.org |
| schex | [Using schex with Seurat](http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/schex.html) | Freytag, R package 2019 | https://github.com/SaskiaFreytag/schex |
| alevin | [Import alevin counts into Seurat](http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/alevin.html) | Srivastava et. al., Genome Biology 2019 | https://github.com/k3yavi/alevin-Rtools |
| Nebulosa | [Visualization of gene expression with Nebulosa](http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/nebulosa.html) | Jose Alquicira-Hernandez and Joseph E. Powell, _Under Review_ | https://github.com/powellgenomicslab/Nebulosa |
| CIPR | [Using CIPR with human PBMC data](http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/cipr.html) | Ekiz et. al., BMC Bioinformatics 2020 | https://github.com/atakanekiz/CIPR-Package |
| miQC | [Running miQC on Seurat objects](http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/miQC.html) | Hippen et. al., bioRxiv 2021 | https://github.com/greenelab/miQC | 
| tricycle | [Running estimate_cycle_position from tricycle on Seurat Objects](http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/tricycle.html) | Zheng et. al., bioRxiv 2021 | https://www.bioconductor.org/packages/release/bioc/html/tricycle.html |