pbmc_small

A subsetted version of 10X Genomics' 3k PBMC dataset

datasets

Defines S4 classes for single-cell genomic data and associated
information, such as dimensionality reduction embeddings, nearest-neighbor
graphs, and spatially-resolved coordinates. Provides data access methods and
R-native hooks to ensure the Seurat object is familiar to other R users. See
Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>,
Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>,
and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>,
Hao Y, Hao S, et al (2021) <doi:10.1016/j.cell.2021.04.048> and
Hao Y, et al (2023) <doi:10.1101/2022.02.24.481684> for
more details.

Paul Hoffman

SeuratObject

Data Structures for Single Cell Data

Rahul Satija

David Collins

Yuhan Hao

Austin Hartman

Gesmira Molla

Andrew Butler

Tim Stuart

Madeline Kowalski

Saket Choudhary

Skylar Li

Longda Jiang

Jeff Farrell

Shiwei Zheng

Christoph Hafemeister

Patrick Roelli

pbmc_small function

A Seurat object with the following slots filled<dl>
 <dt>assays</dt>
<dd><ul>
<li>counts - Raw expression data</li>
<li>data - Normalized expression data</li>
<li>scale.data - Scaled expression data</li>
<li>var.features - names of the current features selected as variable</li>
<li>meta.features - Assay level metadata such as mean and variance</li>
</ul></dd> <dt>meta.data</dt>
<dd>Cell level metadata</dd> <dt>active.assay</dt>
<dd>Current default assay</dd> <dt>active.ident</dt>
<dd>Current default idents</dd> <dt>graphs</dt>
<dd>Neighbor graphs computed, currently stores the SNN</dd> <dt>reductions</dt>
<dd>Dimensional reductions: currently PCA and tSNE</dd> <dt>version</dt>
<dd>Seurat version used to create the object</dd> <dt>commands</dt>
<dd>Command history</dd>
</dl>

Format

A small example version of the PBMC dataset — pbmc_small

A Seurat object with the following slots filled<dl>
 <dt>assays</dt>
<dd><ul>
<li>counts - Raw expression data</li>
<li>data - Normalized expression data</li>
<li>scale.data - Scaled expression data</li>
<li>var.features - names of the current features selected as variable</li>
<li>meta.features - Assay level metadata such as mean and variance</li>
</ul></dd>

 <dt>meta.data</dt>
<dd>Cell level metadata</dd>

 <dt>active.assay</dt>
<dd>Current default assay</dd>

 <dt>active.ident</dt>
<dd>Current default idents</dd>

 <dt>graphs</dt>
<dd>Neighbor graphs computed, currently stores the SNN</dd>

 <dt>reductions</dt>
<dd>Dimensional reductions: currently PCA and tSNE</dd>

 <dt>version</dt>
<dd>Seurat version used to create the object</dd>

 <dt>commands</dt>
<dd>Command history</dd>


</dl>

A small example version of the PBMC dataset

pbmc_small: A small example version of the PBMC dataset

Description

Usage

Arguments

Format