scran

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see scran.

Methods for Single-Cell RNA-Seq Data Analysis

Bioconductor version: 3.9

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 <infinite.monkeys.with.keyboards at gmail.com>

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

Installation

To install this package, start R (version "3.6") and enter:


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

BiocManager::install("scran")

For older versions of R, please refer to the appropriate Bioconductor 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	BatchEffect, Clustering, GeneExpression, ImmunoOncology, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version	1.12.1
In Bioconductor since	BioC 3.3 (R-3.3) (8 years)
License	GPL-3
Depends	SingleCellExperiment
Imports	SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp (>= 0.12.14), stats, methods, utils, Matrix, scater, edgeR, limma, dynamicTreeCut, BiocNeighbors, igraph, statmod, DelayedArray, DelayedMatrixStats, BiocSingular, dqrng
System Requirements	C++11
URL

Suggests	testthat, BiocStyle, knitr, beachmat, HDF5Array, irlba, org.Mm.eg.db, DESeq2, monocle, pracma, Biobase, aroma.light
Linking To	Rcpp, beachmat, BH, dqrng
Enhances
Depends On Me
Imports Me	BASiCS, scDD
Suggests Me	CellTrails, clusterExperiment, HCAData, scone, simpleSingleCell, splatter, TabulaMurisData
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	scran_1.12.1.tar.gz
Windows Binary	scran_1.12.1.zip
Mac OS X 10.11 (El Capitan)	scran_1.12.1.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
Old Source Packages for BioC 3.9	Source Archive