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Methods for Single-Cell RNA-Seq Data Analysis

Bioconductor version: Release (3.18)

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, enter citation("scran")):


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if (!require("BiocManager", quietly = TRUE))


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

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


biocViews Clustering, GeneExpression, ImmunoOncology, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.30.2
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL-3
Depends SingleCellExperiment, scuttle
Imports SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, edgeR, limma, igraph, statmod, DelayedArray, DelayedMatrixStats, BiocSingular, bluster, metapod, dqrng, beachmat
System Requirements C++11
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Suggests testthat, BiocStyle, knitr, rmarkdown, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, monocle, Biobase, pheatmap, scater
Linking To Rcpp, beachmat, BH, dqrng, scuttle
Depends On Me OSCA.advanced, OSCA.basic, OSCA.intro, OSCA.multisample, OSCA.workflows, SingleRBook
Imports Me BASiCS, BASiCStan, BayesSpace, BioTIP, celda, ChromSCape, CiteFuse, Dino, FLAMES, IRISFGM, msImpute, mumosa, pipeComp, scDblFinder, scDD, scMerge, scTreeViz, SingleCellSignalR, singleCellTK, Spaniel, spatialHeatmap
Suggests Me APL, batchelor, bluster, CellTrails, clusterExperiment, decontX, destiny, dittoSeq, escheR, ExperimentSubset, fcoex, ggsc, ggspavis, Glimma, glmGamPoi, HCAData, iSEEu, miloR, Nebulosa, nnSVG, PCAtools, raer, schex, scone, scuttle, simpleSingleCell, SingleCellMultiModal, SingleR, splatter, SPOTlight, TabulaMurisData, tidySingleCellExperiment, transformGamPoi, TSCAN, velociraptor, Voyager
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scran_1.30.2.tar.gz
Windows Binary scran_1.30.2.zip
macOS Binary (x86_64) scran_1.30.2.tgz
macOS Binary (arm64) scran_1.30.2.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/
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Old Source Packages for BioC 3.18 Source Archive