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.

Satija Lab

Seurat

Tools for Single Cell Genomics

Rahul Satija

Andrew Butler

Paul Hoffman

Jeff Farrell

Shiwei Zheng

Christoph Hafemeister

Patrick Roelli

pbmc_small function

A Seurat object with the following slots filled<dl class="dl-horizontal">
 <dt>raw.data</dt><dd>Raw expression data</dd>
 <dt>data</dt><dd>Normalized expression data</dd>
 <dt>scale.data</dt><dd>Scaled expression data</dd>
 <dt>var.genes</dt><dd>Variable genes</dd>
 <dt>dr</dt><dd>Dimmensional reductions: currently PCA and tSNE</dd>
 <dt>hvg.info</dt><dd>Information about highly variable genes</dd>
 <dt>cluster.tree</dt><dd>Cluster tree</dd>
 <dt>calc.params</dt><dd>Parameters for calculations done thus far</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>raw.data</dt><dd>Raw expression data</dd>
 <dt>data</dt><dd>Normalized expression data</dd>
 <dt>scale.data</dt><dd>Scaled expression data</dd>
 <dt>var.genes</dt><dd>Variable genes</dd>
 <dt>dr</dt><dd>Dimmensional reductions: currently PCA and tSNE</dd>
 <dt>hvg.info</dt><dd>Information about highly variable genes</dd>
 <dt>cluster.tree</dt><dd>Cluster tree</dd>
 <dt>calc.params</dt><dd>Parameters for calculations done thus far</dd>
</dl>

A small example version of the PBMC dataset

pbmc_small: A small example version of the PBMC dataset

Description

Usage

Arguments

Format