https://github.com/satijalab/seurat-wrappers
Community-provided extensions to Seurat
https://github.com/satijalab/seurat-wrappers
community single-cell-analysis single-cell-genomics
Last synced: 10 days ago
JSON representation
Community-provided extensions to Seurat
- Host: GitHub
- URL: https://github.com/satijalab/seurat-wrappers
- Owner: satijalab
- License: gpl-3.0
- Created: 2019-04-24T17:07:16.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2024-05-22T20:57:19.000Z (11 months ago)
- Last Synced: 2024-05-22T21:59:10.950Z (11 months ago)
- Topics: community, single-cell-analysis, single-cell-genomics
- Language: R
- Homepage:
- Size: 116 MB
- Stars: 284
- Watchers: 12
- Forks: 126
- Open Issues: 87
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- jimsghstars - satijalab/seurat-wrappers - Community-provided extensions to Seurat (R)
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 |
| PaCMAP | [Running PaCMAP on Seurat Objects](http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/pacmap.html) | Wang et. al, JMLR 2021; Huang et. al, Communications Biology 2022 | https://github.com/YingfanWang/PaCMAP |