CRAN/E | Seurat

Seurat

Tools for Single Cell Genomics

Installation

About

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.

Citation Seurat citation info
satijalab.org/seurat
github.com/satijalab/seurat
Bug report File report

Key Metrics

Version 5.0.3
R ≥ 4.0.0
Published 2024-03-18 32 days ago
Needs compilation? yes
License MIT
License File
CRAN checks Seurat results

Downloads

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Last 30 days 51.792 -20%
Last 90 days 158.183 -6%
Last 365 days 538.806 +15%

Maintainer

Maintainer

Rahul Satija

seurat@nygenome.org

Authors

Andrew Butler

ctb

Saket Choudhary

ctb

Charlotte Darby

ctb

Jeff Farrell

ctb

Isabella Grabski

ctb

Christoph Hafemeister

ctb

Yuhan Hao

ctb

Austin Hartman

ctb

Paul Hoffman

ctb

Jaison Jain

ctb

Longda Jiang

ctb

Madeline Kowalski

ctb

Skylar Li

ctb

Gesmira Molla

ctb

Efthymia Papalexi

ctb

Patrick Roelli

ctb

Rahul Satija

aut / cre

Karthik Shekhar

ctb

Avi Srivastava

ctb

Tim Stuart

ctb

Kristof Torkenczy

ctb

Shiwei Zheng

ctb

Satija Lab
Collaborators

fnd

Material

README
NEWS
Reference manual
Package source

In Views

Omics

Additional repos

satijalab.r-universe.dev
bnprks.r-universe.dev

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

Seurat archive

Depends

R ≥ 4.0.0
methods
SeuratObject ≥ 5.0.0

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
Load all 53 items
(warning: might lead to performance issues and take some time)

Suggests

ape
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

LinkingTo

Rcpp ≥ 0.11.0
RcppEigen
RcppProgress

Reverse Depends

CACIMAR
CelliD
phemd
ReactomeGSA.data
scAnnotatR
SCArray.sat
scCustomize

Reverse Imports

AnanseSeurat
APackOfTheClones
APL
bbknnR
benchdamic
CAMML
CDI
COTAN
CuratedAtlasQueryR
decontX
Dino
DR.SC
DWLS
GeneNMF
ggsc
ggsector
infercnv
mixhvg
nebula
partCNV
pipeComp
Platypus
PRECAST
ProFAST
RegionalST
rPanglaoDB
scAnnotate
scaper
scBFA
scBubbletree
scCB2
sccca
scDataviz
scDiffCom
scFeatures
scfetch
scGate
scGOclust
scMappR
scperturbR
scpoisson
SCRIP
scRNAseqApp
scRNAstat
scTreeViz
SignacX
singleCellTK
SoupX
Spaniel
SPECK
Load all 55 items
(warning: might lead to performance issues and take some time)

Reverse Suggests

ASURAT
BayesSpace
BisqueRNA
Canek
cellpypes
CIARA
ClustAssess
clustifyr
clustifyrdatahub
clustree
combiroc
conos
consICA
countland
CRMetrics
CytoSimplex
DCATS
decoupleR
demuxSNP
DIscBIO
dittoSeq
dorothea
dyngen
EpiMix
escape
escheR
FEAST
fgsea
GeomxTools
grandR
harmony
HCATonsilData
M3Drop
MOFA2
monocle
muscData
Nebulosa
nipalsMCIA
progeny
RESET
rliger
schex
SCORPIUS
SCpubr
scRepertoire
scTensor
Signac
SimBenchData
SimBu
SpatialDecon
Load all 59 items
(warning: might lead to performance issues and take some time)

Reverse Enhances

ReactomeGSA
SeuratObject