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
3.0.1
Date
2019-05-16
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
Additional_repositories
https://mojaveazure.github.io/loomR
Depends
R (>= 3.4.0), methods,
Imports
ape, cluster, cowplot, fitdistrplus, future, future.apply, ggplot2 (>= 3.0.0), ggrepel, ggridges, graphics, grDevices, grid, ica, igraph, irlba, KernSmooth, lmtest, MASS, Matrix (>= 1.2.14), metap, pbapply, plotly, png, RANN, RColorBrewer, Rcpp, reticulate, rlang, ROCR, rsvd, Rtsne, scales, sctransform (>= 0.2.0), SDMTools, stats, tools, tsne, utils
LinkingTo
Rcpp (>= 0.11.0), RcppEigen, RcppProgress
License
GPL-3 | file LICENSE
LazyData
true
Collate
'RcppExports.R' 'generics.R' 'clustering.R' 'visualization.R' 'convenience.R' 'data.R' 'differential_expression.R' 'dimensional_reduction.R' 'integration.R' 'objects.R' 'preprocessing.R' 'tree.R' 'utilities.R' 'zzz.R'
RoxygenNote
6.1.1
Encoding
UTF-8
Suggests
loomR, testthat, hdf5r, S4Vectors, SummarizedExperiment, SingleCellExperiment, MAST, DESeq2, GenomicRanges, GenomeInfoDb, IRanges, rtracklayer
NeedsCompilation
yes
Packaged
2019-05-16 15:24:20 UTC; paul
Author
Rahul Satija [aut] (), Andrew Butler [aut] (), Paul Hoffman [aut, cre] (), Tim Stuart [aut] (), Jeff Farrell [ctb], Shiwei Zheng [ctb] (), Christoph Hafemeister [ctb] (), Patrick Roelli [ctb]
Maintainer
Paul Hoffman
Repository
CRAN
Date/Publication
2019-05-16 16:20:57 UTC

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