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> for
more details.

Paul Hoffman

SeuratObject

Data Structures for Single Cell Data

Rahul Satija

Andrew Butler

Tim Stuart

Jeff Farrell

Shiwei Zheng

Christoph Hafemeister

Patrick Roelli

Yuhan Hao

pbmc_small function

A Seurat object with the following slots filled<dl class="dl-horizontal">
 <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 class='dl-horizontal'>
 <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