pbmc_small

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

datasets

A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. 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 Butler A and Satija R (2017) <doi:10.1101/164889> for more details. Please note: SDMTools is available is available from the CRAN archives with install.packages("https://cran.rstudio.com//src/contrib/Archive/SDMTools/SDMTools_1.1-221.2.tar.gz", repos = NULL); it is not in the standard repositories.

Paul Hoffman

Seurat

Tools for Single Cell Genomics

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