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Methods for Single-Cell RNA-Seq Data Analysis

Bioconductor version: Release (3.19)

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>

Citation (from within R, enter citation("scran")):


To install this package, start R (version "4.4") and enter:

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


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


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 1.32.0
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, 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, BatchQC, BayesSpace, celda, ChromSCape, CiteFuse, Dino, epiregulon, epiregulon.extra, FLAMES, lute, MOSim, msImpute, mumosa, pipeComp, scDblFinder, scDD, scMerge, scTreeViz, SingleCellSignalR, singleCellTK, Spaniel, spatialHeatmap, digitalDLSorteR, mixhvg, SC.MEB, SpatialDDLS
Suggests Me APL, Banksy, batchelor, bluster, CellTrails, clusterExperiment, decontX, destiny, dittoSeq, escape, escheR, ExperimentSubset, ggsc, ggspavis, Glimma, glmGamPoi, iSEEu, miloR, Nebulosa, nnSVG, PCAtools, raer, schex, scone, scuttle, SingleCellAlleleExperiment, SingleR, sketchR, smoothclust, splatter, SPOTlight, tidySingleCellExperiment, tidySpatialExperiment, tpSVG, transformGamPoi, TSCAN, velociraptor, Voyager, HCAData, SingleCellMultiModal, TabulaMurisData, simpleSingleCell, Canek, SCdeconR
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package scran_1.32.0.tar.gz
Windows Binary
macOS Binary (x86_64) scran_1.32.0.tgz
macOS Binary (arm64) scran_1.32.0.tgz
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