https://github.com/satijalab/seurat-data
Dataset distribution for Seurat
https://github.com/satijalab/seurat-data
datasets single-cell single-cell-genomics
Last synced: about 2 months ago
JSON representation
Dataset distribution for Seurat
- Host: GitHub
- URL: https://github.com/satijalab/seurat-data
- Owner: satijalab
- License: gpl-3.0
- Created: 2019-05-29T19:43:16.000Z (about 6 years ago)
- Default Branch: main
- Last Pushed: 2025-03-06T19:14:24.000Z (3 months ago)
- Last Synced: 2025-03-29T03:01:51.052Z (2 months ago)
- Topics: datasets, single-cell, single-cell-genomics
- Language: R
- Homepage:
- Size: 189 KB
- Stars: 136
- Watchers: 8
- Forks: 46
- Open Issues: 37
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# SeuratData
SeuratData is a mechanism for distributing datasets in the form of [Seurat](https://satijalab.org/seurat) objects using R's internal package and data management systems. It represents an easy way for users to get access to datasets that are used in the Seurat vignettes.
### Installation
Installation of SeuratData can be accomplished through [devtools](https://cran.r-project.org/package=devtools)
```R
devtools::install_github('satijalab/seurat-data')
```
### Getting Started
When loading SeuratData, a list of all available datasets will be displayed (this is similar to other metapackages like [tidyverse](https://cran.r-project.org/package=tidyverse) along with the version of [Seurat](https://satijalab.org/seurat/) used to create each dataset). This message can be suppressed with [`suppressPackageStartupMessages`](https://stat.ethz.ch/R-manual/R-devel/library/base/html/message.html)
```R
> library(SeuratData)
── Installed datasets ───────────────────────────────────────────────────────────── SeuratData v0.1.0 ──
✔ cbmc 3.0.0 ✔ panc8 3.0.0
✔ ifnb 3.0.0 ✔ pbmc3k 3.0.0
───────────────────────────────────────────────── Key ──────────────────────────────────────────────────
✔ Dataset loaded successfully
```
To see a manifest of all available datasets, use `AvailableData`; this manifest will update as new datasets are uploaded to our data repository.
```R
> AvailableData()
Dataset Version Summary species system ncells tech notes Installed InstalledVersion
cbmc.SeuratData cbmc 3.0.0 scRNAseq and 13-antibody sequencing of CBMCs human CBMC (cord blood) 8617 CITE-seq TRUE 3.0.0
hcabm40k.SeuratData hcabm40k 3.0.0 40,000 Cells From the Human Cell Atlas ICA Bone Marrow Dataset human bone marrow 40000 10x v2 FALSE 3.0.0
ifnb.SeuratData ifnb 3.0.0 IFNB-Stimulated and Control PBMCs human PBMC 13999 10x v1 TRUE 3.0.0
panc8.SeuratData panc8 3.0.0 Eight Pancreas Datasets Across Five Technologies human Pancreatic Islets 14892 SMARTSeq2, Fluidigm C1, CelSeq, CelSeq2, inDrops TRUE 3.0.0
pbmc3k.SeuratData pbmc3k 3.0.0 3k PBMCs from 10X Genomics human PBMC 2700 10x v1 TRUE 3.0.0
pbmcsca.SeuratData pbmcsca 3.0.0 Broad Institute PBMC Systematic Comparative Analysis human PBMC 31021 10x v2, 10x v3, SMARTSeq2, Seq-Well, inDrops, Drop-seq, CelSeq2 HCA benchmark FALSE 3.0.0
```
Installation of datasets can be done with `InstallData`; this function will accept either a dataset name (eg. `pbmc3k`) or the corresponding package name (eg. `pbmc3k.SeuratData`). `InstallData` will automatically attach the installed dataset package so one can immediately load and use the dataset.
```R
> InstallData("pbmc3k")
```
Loading a dataset is done using the [`data`](https://stat.ethz.ch/R-manual/R-devel/library/utils/html/data.html) function
```R
> data("pbmc3k")
> pbmc3k
An object of class Seurat
13714 features across 2700 samples within 1 assay
Active assay: RNA (13714 features)
```
### Dataset documentation and information
All datasets provided have help pages built for them. These pages are accessed using the standard [`help`](https://stat.ethz.ch/R-manual/R-devel/library/utils/html/help.html) function
```R
> ?pbmc3k
> ?ifnb
```
A full command list for the steps taken to generate each dataset is present in the examples section of these help pages.
Packages will also often have citation information bundled with the package. Citation information can be accessed by passing the **package name**, not the dataset name, to the [`citation`](https://stat.ethz.ch/R-manual/R-devel/library/utils/html/citation.html) function
```R
> citation('cbmc.SeuratData')
To cite the CBMC dataset, please use:
Stoeckius et al. Simultaneous epitope and transcriptome measurement in
single cells. Nature Methods (2017)
A BibTeX entry for LaTeX users is
@Article{,
author = {Marlon Stoeckius and Christoph Hafemeister and William Stephenson and Brian Houck-Loomis and Pratip K Chattopadhyay and Harold Swerdlow and Rahul Satija and Peter Smibert},
title = {Simultaneous epitope and transcriptome measurement in single cells},
journal = {Nature Methods},
year = {2017},
doi = {10.1038/nmeth.4380},
url = {https://www.nature.com/articles/nmeth.4380},
}
```
### Rationale and Implementation
We created SeuratData in order to distribute datasets for [Seurat](https://satijalab.org/seurat/get_started.html) [vignettes](https://satijalab.org/seurat/frv.html) in as painless and reproducible a way as possible. We also wanted to give users the flexibility to selectively install and load datasets of interest, to minimize disk storage and memory use.
To accomplish this, we opted to distribute datasets through individual R packages. Under the hood, SeuratData uses and extends standard R functions, such as [`install.packages`](https://stat.ethz.ch/R-manual/R-devel/library/utils/html/install.packages.html) for dataset installation, [`available.packages`](https://stat.ethz.ch/R-manual/R-devel/library/utils/html/available.packages.html) for dataset listing, and [`data`](https://stat.ethz.ch/R-manual/R-devel/library/utils/html/data.html) for dataset loading.
SeuratData therefore serves as a more specific package manager (similar to a metapackage) for R. We provide wrappers around R's package management functions, [extend them to provide relevant metadata](https://github.com/satijalab/seurat-data/#getting-started) about each dataset, and set default settings (for example, the repository where data is stored) to facilitate easy installation.