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 4.3.0
R ≥ 4.0.0
Published 2022-11-18 125 days ago
Needs compilation? yes
License MIT
License File
CRAN checks Seurat results

Downloads

Last 24 hours 0 -100%
Last 7 days 7.881 -31%
Last 30 days 37.965 +1%
Last 90 days 103.139 -23%
Last 365 days 456.210 +31%

Maintainer

Maintainer

Paul Hoffman

seurat@nygenome.org

Authors

Andrew Butler

ctb

Saket Choudhary

ctb

Charlotte Darby

ctb

Jeff Farrell

ctb

Christoph Hafemeister

ctb

Yuhan Hao

ctb

Austin Hartman

ctb

Paul Hoffman

aut / cre

Jaison Jain

ctb

Madeline Kowalski

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
Collaborators

fnd

Material

README
NEWS
Reference manual
Package source

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

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

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 ≥ 1.5-0
matrixStats
miniUI
patchwork
pbapply
plotly ≥ 4.9.0
png
progressr
RANN
RColorBrewer
Rcpp ≥ 1.0.7
RcppAnnoy ≥ 0.0.18
reticulate
rlang
ROCR
Rtsne
scales
scattermore ≥ 0.7
sctransform ≥ 0.3.5
SeuratObject ≥ 4.1.3
shiny
spatstat.explore
spatstat.geom
stats
tibble
tools
utils
uwot ≥ 0.1.14

Suggests

ape
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

LinkingTo

Rcpp ≥ 0.11.0
RcppEigen
RcppProgress

Reverse Depends

CACIMAR
CelliD
ReactomeGSA.data
scAlign
scAnnotatR
schex

Reverse Imports

APL
bbknnR
benchdamic
CAMML
CIDER
CSCDRNA
Dino
DR.SC
DUBStepR
DWLS
infercnv
IRISFGM
maple
mixhvg
Nebulosa
PALMO
pipeComp
Platypus
PRECAST
rPanglaoDB
scBFA
scBubbletree
scCB2
scDataviz
scDiffCom
scMAGeCK
scMappR
scpoisson
SCRIP
scRNAstat
scTreeViz
SignacX
singleCellTK
SoupX
Spaniel
SPECK
SpotClean
spruce
stJoincount
tidyseurat

Reverse Suggests

ASURAT
BayesSpace
BisqueRNA
Canek
cellpypes
CIARA
ClustAssess
clustifyr
clustifyrdatahub
clustree
conos
countland
decoupleR
DIscBIO
dittoSeq
dorothea
dyngen
EasyCellType
EpiMix
escape
fcoex
FEAST
GeomxTools
grandR
harmony
M3Drop
MOFA2
monocle
muscData
progeny
rliger
SCpubr
scRepertoire
scTensor
Signac
SimBenchData
SimBu
SPOTlight
TAPseq
TCGAbiolinks
tidybulk
treefit
tricycle
UCell
VAM

Reverse Enhances

ReactomeGSA