DOI: 10.18129/B9.bioc.scran    

Methods for Single-Cell RNA-Seq Data Analysis

Bioconductor version: Release (3.6)

Implements a variety of low-level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell-specific biases, assignment of cell cycle phase, and detection of highly variable and significantly correlated genes.

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

Maintainer: Aaron Lun <alun at>

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


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


HTML R Script Using scran to perform basic analyses of single-cell RNA-seq data
PDF   Reference Manual
Text   NEWS


biocViews BatchEffect, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.6.9
In Bioconductor since BioC 3.3 (R-3.3) (2 years)
License GPL-3
Depends R (>= 3.4), BiocParallel, SingleCellExperiment
Imports SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp (>= 0.12.14), stats, methods, utils, graphics, grDevices, Matrix, scater, edgeR, limma, dynamicTreeCut, FNN, igraph, shiny, zoo, statmod, ggplot2, DT, viridis
LinkingTo beachmat, Rcpp, Rhdf5lib
Suggests testthat, BiocStyle, knitr, beachmat, HDF5Array, limSolve,, DESeq2, monocle, Rtsne, pracma, Biobase, irlba, aroma.light
SystemRequirements C++11
Depends On Me
Imports Me BASiCS, scDD
Suggests Me scone, splatter
Build Report  

Package Archives

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

Source Package scran_1.6.9.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.11 (El Capitan) scran_1.6.9.tgz
Source Repository git clone
Package Short Url
Package Downloads Report Download Stats
Old Source Packages for BioC 3.6 Source Archive

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: