Seurat

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) tools:::Rd_expr_doi("10.1038/nbt.3192"), Macosko E, Basu A, Satija R, et al (2015) tools:::Rd_expr_doi("10.1016/j.cell.2015.05.002"), Stuart T, Butler A, et al (2019) tools:::Rd_expr_doi("10.1016/j.cell.2019.05.031"), and Hao, Hao, et al (2020) tools:::Rd_expr_doi("10.1101/2020.10.12.335331") for more details.

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>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.

Paul Hoffman

Tools for Single Cell Genomics

Andrew Butler

Saket Choudhary

Charlotte Darby

Jeff Farrell

Christoph Hafemeister

Yuhan Hao

Austin Hartman

Jaison Jain

Madeline Kowalski

Efthymia Papalexi

Patrick Roelli

Rahul Satija

Karthik Shekhar

Avi Srivastava

Tim Stuart

Kristof Torkenczy

Shiwei Zheng

Satija Lab and Collaborators 

Seurat-package function

Seurat uses the following [options()] to configure behaviour:
<dl>
 <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 availability is not a concern.</dd> <dt><code>Seurat.warn.umap.uwot</code></dt>
<dd>Show warning about the default backend
 for <code>RunUMAP</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> <dt><code>Seurat.limma.wilcox.msg</code></dt>
<dd>Show message about more efficient
 Wilcoxon Rank Sum test available via the limma package</dd> <dt><code>Seurat.Rfast2.msg</code></dt>
<dd>Show message about more efficient
 Moran's I function available via the Rfast2 package</dd> <dt><code>Seurat.warn.vlnplot.split</code></dt>
<dd>Show message about changes to
 default behavior of split/multi violin plots</dd>
</dl>

Package options

Maintainer: Paul Hoffman <a href="/link/seurat%40nygenome.org?package=Seurat&version=4.3.0.1" data-mini-rdoc="Seurat::seurat@nygenome.org">seurat@nygenome.org</a> (<a href="https://orcid.org/0000-0002-7693-8957">ORCID</a>)
Other contributors:<ul>
<li>Andrew Butler <a href="/link/abutler%40nygenome.org?package=Seurat&version=4.3.0.1" data-mini-rdoc="Seurat::abutler@nygenome.org">abutler@nygenome.org</a> (<a href="https://orcid.org/0000-0003-3608-0463">ORCID</a>) [contributor]</li>
<li>Saket Choudhary <a href="/link/schoudhary%40nygenome.org?package=Seurat&version=4.3.0.1" data-mini-rdoc="Seurat::schoudhary@nygenome.org">schoudhary@nygenome.org</a> (<a href="https://orcid.org/0000-0001-5202-7633">ORCID</a>) [contributor]</li>
<li>Charlotte Darby <a href="/link/cdarby%40nygenome.org?package=Seurat&version=4.3.0.1" data-mini-rdoc="Seurat::cdarby@nygenome.org">cdarby@nygenome.org</a> (<a href="https://orcid.org/0000-0003-2195-5300">ORCID</a>) [contributor]</li>
<li>Jeff Farrell <a href="/link/jfarrell%40g.harvard.edu?package=Seurat&version=4.3.0.1" data-mini-rdoc="Seurat::jfarrell@g.harvard.edu">jfarrell@g.harvard.edu</a> [contributor]</li>
<li>Christoph Hafemeister <a href="/link/chafemeister%40nygenome.org?package=Seurat&version=4.3.0.1" data-mini-rdoc="Seurat::chafemeister@nygenome.org">chafemeister@nygenome.org</a> (<a href="https://orcid.org/0000-0001-6365-8254">ORCID</a>) [contributor]</li>
<li>Yuhan Hao <a href="/link/yhao%40nygenome.org?package=Seurat&version=4.3.0.1" data-mini-rdoc="Seurat::yhao@nygenome.org">yhao@nygenome.org</a> (<a href="https://orcid.org/0000-0002-1810-0822">ORCID</a>) [contributor]</li>
<li>Jaison Jain <a href="/link/jjain%40nygenome.org?package=Seurat&version=4.3.0.1" data-mini-rdoc="Seurat::jjain@nygenome.org">jjain@nygenome.org</a> (<a href="https://orcid.org/0000-0002-9478-5018">ORCID</a>) [contributor]</li>
<li>Efthymia Papalexi <a href="/link/epapalexi%40nygenome.org?package=Seurat&version=4.3.0.1" data-mini-rdoc="Seurat::epapalexi@nygenome.org">epapalexi@nygenome.org</a> (<a href="https://orcid.org/0000-0001-5898-694X">ORCID</a>) [contributor]</li>
<li>Patrick Roelli <a href="/link/proelli%40nygenome.org?package=Seurat&version=4.3.0.1" data-mini-rdoc="Seurat::proelli@nygenome.org">proelli@nygenome.org</a> [contributor]</li>
<li>Rahul Satija <a href="/link/rsatija%40nygenome.org?package=Seurat&version=4.3.0.1" data-mini-rdoc="Seurat::rsatija@nygenome.org">rsatija@nygenome.org</a> (<a href="https://orcid.org/0000-0001-9448-8833">ORCID</a>) [contributor]</li>
<li>Karthik Shekhar <a href="/link/kshekhar%40berkeley.edu?package=Seurat&version=4.3.0.1" data-mini-rdoc="Seurat::kshekhar@berkeley.edu">kshekhar@berkeley.edu</a> [contributor]</li>
<li>Avi Srivastava <a href="/link/asrivastava%40nygenome.org?package=Seurat&version=4.3.0.1" data-mini-rdoc="Seurat::asrivastava@nygenome.org">asrivastava@nygenome.org</a> (<a href="https://orcid.org/0000-0001-9798-2079">ORCID</a>) [contributor]</li>
<li>Tim Stuart <a href="/link/tstuart%40nygenome.org?package=Seurat&version=4.3.0.1" data-mini-rdoc="Seurat::tstuart@nygenome.org">tstuart@nygenome.org</a> (<a href="https://orcid.org/0000-0002-3044-0897">ORCID</a>) [contributor]</li>
<li>Kristof Torkenczy (<a href="https://orcid.org/0000-0002-4869-7957">ORCID</a>) [contributor]</li>
<li>Shiwei Zheng <a href="/link/szheng%40nygenome.org?package=Seurat&version=4.3.0.1" data-mini-rdoc="Seurat::szheng@nygenome.org">szheng@nygenome.org</a> (<a href="https://orcid.org/0000-0001-6682-6743">ORCID</a>) [contributor]</li>
<li>Satija Lab and Collaborators [funder]</li>
</ul>

Author

Seurat: Tools for Single Cell Genomics — Seurat-package

Seurat uses the following [options()] to configure behaviour:
<dl>
 <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 availability is not a concern.</dd>

 <dt><code>Seurat.warn.umap.uwot</code></dt>
<dd>Show warning about the default backend
 for <code>RunUMAP</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>

 <dt><code>Seurat.limma.wilcox.msg</code></dt>
<dd>Show message about more efficient
 Wilcoxon Rank Sum test available via the limma package</dd>

 <dt><code>Seurat.Rfast2.msg</code></dt>
<dd>Show message about more efficient
 Moran's I function available via the Rfast2 package</dd>

 <dt><code>Seurat.warn.vlnplot.split</code></dt>
<dd>Show message about changes to
 default behavior of split/multi violin plots</dd>


</dl>

Maintainer: Paul Hoffman <a href='mailto:seurat@nygenome.org'>seurat@nygenome.org</a> (<a href='https://orcid.org/0000-0002-7693-8957'>ORCID</a>)
Other contributors:<ul>
<li>Andrew Butler <a href='mailto:abutler@nygenome.org'>abutler@nygenome.org</a> (<a href='https://orcid.org/0000-0003-3608-0463'>ORCID</a>) [contributor]</li>
<li>Saket Choudhary <a href='mailto:schoudhary@nygenome.org'>schoudhary@nygenome.org</a> (<a href='https://orcid.org/0000-0001-5202-7633'>ORCID</a>) [contributor]</li>
<li>Charlotte Darby <a href='mailto:cdarby@nygenome.org'>cdarby@nygenome.org</a> (<a href='https://orcid.org/0000-0003-2195-5300'>ORCID</a>) [contributor]</li>
<li>Jeff Farrell <a href='mailto:jfarrell@g.harvard.edu'>jfarrell@g.harvard.edu</a> [contributor]</li>
<li>Christoph Hafemeister <a href='mailto:chafemeister@nygenome.org'>chafemeister@nygenome.org</a> (<a href='https://orcid.org/0000-0001-6365-8254'>ORCID</a>) [contributor]</li>
<li>Yuhan Hao <a href='mailto:yhao@nygenome.org'>yhao@nygenome.org</a> (<a href='https://orcid.org/0000-0002-1810-0822'>ORCID</a>) [contributor]</li>
<li>Jaison Jain <a href='mailto:jjain@nygenome.org'>jjain@nygenome.org</a> (<a href='https://orcid.org/0000-0002-9478-5018'>ORCID</a>) [contributor]</li>
<li>Efthymia Papalexi <a href='mailto:epapalexi@nygenome.org'>epapalexi@nygenome.org</a> (<a href='https://orcid.org/0000-0001-5898-694X'>ORCID</a>) [contributor]</li>
<li>Patrick Roelli <a href='mailto:proelli@nygenome.org'>proelli@nygenome.org</a> [contributor]</li>
<li>Rahul Satija <a href='mailto:rsatija@nygenome.org'>rsatija@nygenome.org</a> (<a href='https://orcid.org/0000-0001-9448-8833'>ORCID</a>) [contributor]</li>
<li>Karthik Shekhar <a href='mailto:kshekhar@berkeley.edu'>kshekhar@berkeley.edu</a> [contributor]</li>
<li>Avi Srivastava <a href='mailto:asrivastava@nygenome.org'>asrivastava@nygenome.org</a> (<a href='https://orcid.org/0000-0001-9798-2079'>ORCID</a>) [contributor]</li>
<li>Tim Stuart <a href='mailto:tstuart@nygenome.org'>tstuart@nygenome.org</a> (<a href='https://orcid.org/0000-0002-3044-0897'>ORCID</a>) [contributor]</li>
<li>Kristof Torkenczy (<a href='https://orcid.org/0000-0002-4869-7957'>ORCID</a>) [contributor]</li>
<li>Shiwei Zheng <a href='mailto:szheng@nygenome.org'>szheng@nygenome.org</a> (<a href='https://orcid.org/0000-0001-6682-6743'>ORCID</a>) [contributor]</li>
<li>Satija Lab and Collaborators [funder]</li>
</ul>

Seurat: Tools for Single Cell Genomics

Seurat-package: Seurat: Tools for Single Cell Genomics

Description

Arguments

Package options

Author

See Also