Seurat

Tools for Single Cell Genomics

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.

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Description file content

Package
Seurat
Version
2.1.0
Date
2017-10-11
Title
Tools for Single Cell Genomics
Description
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) , Macosko E, Basu A, Satija R, et al (2015) , and Butler A and Satija R (2017) for more details.
URL
BugReports
https://github.com/satijalab/seurat/issues
Depends
R (>= 3.2.0), ggplot2, cowplot, Matrix,
SystemRequirements
Java (>= 1.6)
Imports
methods, ROCR, stringr, mixtools, lars, ica, tsne, Rtsne, fpc, ape, VGAM, pbapply, igraph, FNN, caret, dplyr, RColorBrewer, MASS, irlba, reshape2, gridExtra, gplots, gdata, Rcpp, tclust, ranger, NMF, dtw, SDMTools, plotly, diffusionMap, Hmisc, tidyr, ggjoy
LinkingTo
Rcpp, RcppEigen, RcppProgress
License
GPL-3 | file LICENSE
LazyData
true
Collate
'RcppExports.R' 'seurat.R' 'cluster_determination.R' 'cluster_determination_internal.R' 'cluster_validation.R' 'data.R' 'deprecated_functions.R' 'differential_expression.R' 'differential_expression_internal.R' 'dimensional_reduction.R' 'dimensional_reduction_internal.R' 'dimensional_reduction_utilities.R' 'interaction.R' 'jackstraw.R' 'jackstraw_internal.R' 'multi_modal.R' 'plotting.R' 'plotting_internal.R' 'plotting_utilities.R' 'preprocessing.R' 'preprocessing_internal.R' 'printing_utilities.R' 'scoring.R' 'snn.R' 'spatial.R' 'spatial_internal.R' 'tSNE_project.R' 'utilities.R' 'utilities_internal.R'
RoxygenNote
6.0.1
Suggests
testthat, SummarizedExperiment, MAST, DESeq2
NeedsCompilation
yes
Packaged
2017-10-12 15:52:19 UTC; paul
Author
Rahul Satija [aut], Andrew Butler [aut], Paul Hoffman [aut, cre], Jeff Farrell [ctb], Shiwei Zheng [ctb], Christoph Hafemeister [ctb], Patrick Roelli [ctb]
Maintainer
Paul Hoffman
Repository
CRAN
Date/Publication
2017-10-12 20:36:51 UTC

install.packages('Seurat')

2.1.0

a month ago

http://www.satijalab.org/seurat

Paul Hoffman

GPL-3 | file LICENSE

Depends on

R (>= 3.2.0), ggplot2, cowplot, Matrix,

Imports

methods, ROCR, stringr, mixtools, lars, ica, tsne, Rtsne, fpc, ape, VGAM, pbapply, igraph, FNN, caret, dplyr, RColorBrewer, MASS, irlba, reshape2, gridExtra, gplots, gdata, Rcpp, tclust, ranger, NMF, dtw, SDMTools, plotly, diffusionMap, Hmisc, tidyr, ggjoy

Suggests

testthat, SummarizedExperiment, MAST, DESeq2

Discussions