Seurat-package

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

Seurat-package function

Seurat uses the following [options()] to configure behaviour:<dl class="dl-horizontal">
 <dt><code>Seurat.memsafe</code></dt><dd>global option to call gc() after many operations.
 This can be helpful in cleaning up the memory status of the R session and
 prevent use of swap space. However, it does add to the computational overhead
 and setting to FALSE can speed things up if you're working in an environment
 where RAM availabiliy is not a concern.</dd>
 <dt><code>Seurat.warn.umap.uwot</code></dt><dd>Show warning about the default backend
 for <code><a rd-options="" href="/link/RunUMAP?package=Seurat&version=3.1.4" data-mini-rdoc="Seurat::RunUMAP">RunUMAP</a></code> changing from Python UMAP via reticulate to UWOT</dd>
 <dt><code>Seurat.checkdots</code></dt><dd>For functions that have ... as a parameter,
 this controls the behavior when an item isn't used. Can be one of warn,
 stop, or silent.</dd>
</dl>

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Tools for single-cell genomics — Seurat-package

Tools for single-cell genomics

Seurat-package: Tools for single-cell genomics

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