Seurat-package | R Documentation |
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) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/nbt.3192")}, Macosko E, Basu A, Satija R, et al (2015) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.cell.2015.05.002")}, Stuart T, Butler A, et al (2019) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.cell.2019.05.031")}, and Hao, Hao, et al (2020) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1101/2020.10.12.335331")} for more details.
Seurat uses the following [options()] to configure behaviour:
Seurat.memsafe
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.
Seurat.warn.umap.uwot
Show warning about the default backend
for RunUMAP
changing from Python UMAP via reticulate to UWOT
Seurat.checkdots
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.
Seurat.limma.wilcox.msg
Show message about more efficient Wilcoxon Rank Sum test available via the limma package
Seurat.Rfast2.msg
Show message about more efficient Moran's I function available via the Rfast2 package
Seurat.warn.vlnplot.split
Show message about changes to default behavior of split/multi violin plots
Maintainer: Rahul Satija seurat@nygenome.org (ORCID)
Other contributors:
Andrew Butler abutler@nygenome.org (ORCID) [contributor]
Saket Choudhary schoudhary@nygenome.org (ORCID) [contributor]
David Collins dcollins@nygenome.org (ORCID) [contributor]
Charlotte Darby cdarby@nygenome.org (ORCID) [contributor]
Jeff Farrell jfarrell@g.harvard.edu [contributor]
Isabella Grabski igrabski@nygenome.org (ORCID) [contributor]
Christoph Hafemeister chafemeister@nygenome.org (ORCID) [contributor]
Yuhan Hao yhao@nygenome.org (ORCID) [contributor]
Austin Hartman ahartman@nygenome.org (ORCID) [contributor]
Paul Hoffman hoff0792@umn.edu (ORCID) [contributor]
Jaison Jain jjain@nygenome.org (ORCID) [contributor]
Longda Jiang ljiang@nygenome.org (ORCID) [contributor]
Madeline Kowalski mkowalski@nygenome.org (ORCID) [contributor]
Skylar Li sli@nygenome.org [contributor]
Gesmira Molla gmolla@nygenome.org (ORCID) [contributor]
Efthymia Papalexi epapalexi@nygenome.org (ORCID) [contributor]
Patrick Roelli proelli@nygenome.org [contributor]
Karthik Shekhar kshekhar@berkeley.edu [contributor]
Avi Srivastava asrivastava@nygenome.org (ORCID) [contributor]
Tim Stuart tstuart@nygenome.org (ORCID) [contributor]
Kristof Torkenczy (ORCID) [contributor]
Shiwei Zheng szheng@nygenome.org (ORCID) [contributor]
Satija Lab and Collaborators [funder]
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