scran

This is thereleased version of scran; for the devel version, seescran.

Methods for Single-Cell RNA-Seq Data Analysis

DOI: 10.18129/B9.bioc.scran

Bioconductor version: Release (3.22)

Implements miscellaneous functions for interpretation of single-cell RNA-seq data. Methods are provided for assignment of cell cycle phase, detection of highly variable and significantly correlated genes, identification of marker genes, and other common tasks in routine single-cell analysis workflows.

Author: Aaron Lun [aut, cre], Karsten Bach [aut], Jong Kyoung Kim [ctb], Antonio Scialdone [ctb]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

Citation (from within R, entercitation("scran")):

Installation

To install this package, start R (version "4.5") and enter:

if (!require("BiocManager", quietly = TRUE))    install.packages("BiocManager")BiocManager::install("scran")

For older versions of R, please refer to the appropriateBioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scran")

Using scran to analyze scRNA-seq data	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Clustering,GeneExpression,ImmunoOncology,Normalization,RNASeq,Sequencing,SingleCell,Software,Transcriptomics
Version	1.38.0
In Bioconductor since	BioC 3.3 (R-3.3) (9.5 years)
License	GPL-3
Depends	SingleCellExperiment,scuttle
Imports	SummarizedExperiment,S4Vectors,BiocGenerics,BiocParallel,Rcpp, stats, methods, utils,Matrix,edgeR,limma,igraph,statmod,MatrixGenerics,S4Arrays,DelayedArray,BiocSingular,bluster,metapod,dqrng,beachmat
System Requirements	C++11
URL	https://github.com/MarioniLab/scran/
Bug Reports	https://github.com/MarioniLab/scran/issues

Suggests	testthat,BiocStyle,knitr,rmarkdown,DelayedMatrixStats,HDF5Array,scRNAseq,dynamicTreeCut,ResidualMatrix,ScaledMatrix,DESeq2,pheatmap,scater
Linking To	Rcpp,beachmat,BH,dqrng,scuttle
Enhances
Depends On Me	OSCA.advanced, OSCA.basic, OSCA.intro, OSCA.multisample, OSCA.workflows, SingleRBook
Imports Me	BASiCS,BASiCStan,BatchQC,BayesSpace,BioTIP,celda,chevreulPlot,chevreulProcess,ChromSCape,CiteFuse,Coralysis,DeconvoBuddies,Dino,epiregulon,epiregulon.extra,FLAMES,MOSim,MPAC,msImpute,mumosa,pipeComp,scDblFinder,scDD,scMerge,scTreeViz,singleCellTK,Spaniel,SpaNorm, OSTA,mixhvg
Suggests Me	anglemania,APL,Banksy,batchelor,blase,bluster,CellTrails,clusterExperiment,decontX,destiny,dittoSeq,DOtools,escape,escheR,ExperimentSubset,ggsc,ggspavis,Glimma,glmGamPoi,GSVA,iSEEu,jazzPanda,miloR,Nebulosa,nnSVG,raer,ReactomeGSA,scDiagnostics,scDotPlot,schex,scLANE,scone,scuttle,simPIC,SingleCellAlleleExperiment,sketchR,smoothclust,splatter,SPOTlight,StabMap,SuperCellCyto,SVP,tidySingleCellExperiment,tpSVG,transformGamPoi,TSCAN,velociraptor,Voyager,HCAData,SingleCellMultiModal,TabulaMurisData,simpleSingleCell,Canek,SCdeconR
Links To Me
Build Report	Build Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source Package	scran_1.38.0.tar.gz
Windows Binary (x86_64)	scran_1.38.0.zip (64-bit only)
macOS Binary (x86_64)	scran_1.38.0.tgz
macOS Binary (arm64)	scran_1.38.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scran
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scran
Bioc Package Browser	https://code.bioconductor.org/browse/scran/
Package Short Url	https://bioconductor.org/packages/scran/
Package Downloads Report	Download Stats

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