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 wehi.edu.au>

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

Installation

To install this package, start R (version "3.5") 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 perform basic analyses of single-cell RNA-seq data HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BatchEffect, Clustering, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.8.4
In Bioconductor since BioC 3.3 (R-3.3) (8 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
System Requirements C++11
URL
See More
Suggests testthat, BiocStyle, knitr, beachmat, HDF5Array, limSolve, org.Mm.eg.db, DESeq2, monocle, pracma, Biobase, irlba, aroma.light
Linking To beachmat, Rcpp, Rhdf5lib
Enhances
Depends On Me simpleSingleCell
Imports Me BASiCS, scDD
Suggests Me scone, splatter
Links To Me
Build Report Build Report

Package Archives

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

Source Package scran_1.8.4.tar.gz
Windows Binary scran_1.8.4.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) scran_1.8.4.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 3.7 Source Archive