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: |
4.1.1 |
| Depends: |
R (≥ 4.0.0), methods |
| Imports: |
cluster, cowplot, fitdistrplus, future, future.apply, ggplot2 (≥ 3.3.0), ggrepel, ggridges, graphics, grDevices, grid, httr, ica, igraph, irlba, jsonlite, KernSmooth, leiden (≥ 0.3.1), lmtest, MASS, Matrix (≥ 1.2-14), matrixStats, miniUI, patchwork, pbapply, plotly (≥ 4.9.0), png, RANN, RColorBrewer, Rcpp (≥ 1.0.7), RcppAnnoy (≥ 0.0.18), reticulate, rlang, ROCR, Rtsne, scales, scattermore (≥ 0.7), sctransform (≥
0.3.3), SeuratObject (≥ 4.1.0), shiny, spatstat.core, spatstat.geom, stats, tibble, tools, utils, uwot (≥ 0.1.9) |
| LinkingTo: |
Rcpp (≥ 0.11.0), RcppEigen, RcppProgress |
| Suggests: |
ape, rsvd, testthat, hdf5r, S4Vectors, SummarizedExperiment, SingleCellExperiment, MAST, DESeq2, BiocGenerics, GenomicRanges, GenomeInfoDb, IRanges, rtracklayer, Rfast2, monocle, Biobase, VGAM, limma, metap, enrichR, mixtools, ggrastr |
| Published: |
2022-05-02 |
| Author: |
Andrew Butler 
[ctb],
Saket Choudhary
[ctb],
Charlotte Darby
[ctb],
Jeff Farrell [ctb],
Christoph Hafemeister
[ctb],
Yuhan Hao [ctb],
Paul Hoffman
[aut, cre],
Jaison Jain [ctb],
Efthymia Papalexi
[ctb],
Patrick Roelli [ctb],
Rahul Satija
[ctb],
Karthik Shekhar [ctb],
Avi Srivastava
[ctb],
Tim Stuart [ctb],
Kristof Torkenczy
[ctb],
Shiwei Zheng
[ctb],
Satija Lab and Collaborators [fnd] |
| Maintainer: |
Paul Hoffman <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 |
| Citation: |
Seurat citation info |
| Materials: |
README NEWS |
| CRAN checks: |
Seurat results |
| Reverse depends: |
CACIMAR, CelliD, phemd, ReactomeGSA.data, scAlign, scAnnotatR, schex |
| Reverse imports: |
APL, bbknnR, benchdamic, CAMML, CIDER, CSCDRNA, Dino, DR.SC, DUBStepR, DWLS, IRISFGM, maple, Nebulosa, PALMO, pipeComp, Platypus, PRECAST, rPanglaoDB, scAnnotate, scBFA, scCB2, scDataviz, scDiffCom, scMAGeCK, scMappR, scpoisson, SCRIP, scRNAstat, scTreeViz, SignacX, singleCellTK, SoupX, Spaniel, spruce, tidyseurat |
| Reverse suggests: |
ASURAT, BayesSpace, BisqueRNA, Canek, cellpypes, CIARA, ClustAssess, clustifyrdatahub, clustree, conos, countland, decoupleR, DIscBIO, dittoSeq, dorothea, escape, fcoex, FEAST, GeomxTools, harmony, M3Drop, MOFA2, monocle, muscData, progeny, rliger, Rmagic, scRepertoire, scTensor, Signac, SimBenchData, SPOTlight, TAPseq, TCGAbiolinks, tidybulk, treefit, tricycle, UCell, VAM |
| Reverse enhances: |
ReactomeGSA |