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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.
Version: | 5.1.0 |
Depends: | R (≥ 4.0.0), methods, SeuratObject (≥ 5.0.2) |
Imports: | cluster, cowplot, fastDummies, fitdistrplus, future, future.apply, generics (≥ 0.1.3), ggplot2 (≥ 3.3.0), ggrepel, ggridges, graphics, grDevices, grid, httr, ica, igraph, irlba, jsonlite, KernSmooth, leiden (≥ 0.3.1), lifecycle, lmtest, MASS, Matrix (≥ 1.5-0), matrixStats, miniUI, patchwork, pbapply, plotly (≥ 4.9.0), png, progressr, purrr, RANN, RColorBrewer, Rcpp (≥ 1.0.7), RcppAnnoy (≥ 0.0.18), RcppHNSW, reticulate, rlang, ROCR, RSpectra, Rtsne, scales, scattermore (≥ 1.2), sctransform (≥ 0.4.1), shiny, spatstat.explore, spatstat.geom, stats, tibble, tools, utils, uwot (≥ 0.1.10) |
LinkingTo: | Rcpp (≥ 0.11.0), RcppEigen, RcppProgress |
Suggests: | ape, arrow, BPCells, rsvd, testthat, hdf5r, S4Vectors, SummarizedExperiment, SingleCellExperiment, MAST, DESeq2, BiocGenerics, GenomicRanges, GenomeInfoDb, IRanges, rtracklayer, Rfast2, monocle, Biobase, VGAM, limma, metap, enrichR, mixtools, ggrastr, data.table, R.utils, presto, DelayedArray, harmony |
Published: | 2024-05-10 |
DOI: | 10.32614/CRAN.package.Seurat |
Author: | Andrew Butler |
Maintainer: | Rahul Satija <seurat at nygenome.org> |
BugReports: | https://github.com/satijalab/seurat/issues |
License: | MIT + file LICENSE |
URL: | https://satijalab.org/seurat, https://github.com/satijalab/seurat |
NeedsCompilation: | yes |
Additional_repositories: | https://satijalab.r-universe.dev, https://bnprks.r-universe.dev |
Citation: | Seurat citation info |
Materials: | README NEWS |
In views: | Omics |
CRAN checks: | Seurat results |
Reference manual: | Seurat.pdf |
Package source: | Seurat_5.1.0.tar.gz |
Windows binaries: | r-devel: Seurat_5.1.0.zip, r-release: Seurat_5.1.0.zip, r-oldrel: Seurat_5.1.0.zip |
macOS binaries: | r-release (arm64): Seurat_5.1.0.tgz, r-oldrel (arm64): Seurat_5.1.0.tgz, r-release (x86_64): Seurat_5.1.0.tgz, r-oldrel (x86_64): Seurat_5.1.0.tgz |
Old sources: | Seurat archive |
Please use the canonical form https://CRAN.R-project.org/package=Seurat to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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