DOI: 10.18129/B9.bioc.scran    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see scran.

Methods for Single-Cell RNA-Seq Data Analysis

Bioconductor version: 3.7

Implements functions for low-level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell-specific biases, assignment of cell cycle phase, detection of highly variable and significantly correlated genes, correction of batch effects, identification of marker genes, and other common tasks in single-cell analysis workflows.

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

Maintainer: Aaron Lun <alun at>

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HTML R Script Using scran to perform basic analyses of single-cell RNA-seq data
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biocViews BatchEffect, Clustering, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.8.4
In Bioconductor since BioC 3.3 (R-3.3) (2.5 years)
License GPL-3
Depends R (>= 3.5), BiocParallel, SingleCellExperiment
Imports SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp (>= 0.12.14), stats, methods, utils, graphics, grDevices, Matrix, scater, edgeR, limma, dynamicTreeCut, FNN, igraph, shiny, statmod, ggplot2, DT, viridis, DelayedArray, DelayedMatrixStats
LinkingTo beachmat, Rcpp, Rhdf5lib
Suggests testthat, BiocStyle, knitr, beachmat, HDF5Array, limSolve,, DESeq2, monocle, pracma, Biobase, irlba, aroma.light
SystemRequirements C++11
Depends On Me simpleSingleCell
Imports Me BASiCS, scDD
Suggests Me scone, splatter
Links To Me
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