To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("scran")

In most cases, you don't need to download the package archive at all.

scran

DOI: 10.18129/B9.bioc.scran    

This is the development version of scran; for the stable release version, see scran.

Methods for Single-Cell RNA-Seq Data Analysis

Bioconductor version: Development (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 wehi.edu.au>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("scran")

Documentation

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

Details

biocViews BatchEffect, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.5.12
In Bioconductor since BioC 3.3 (R-3.3) (1.5 years)
License GPL-3
Depends R (>= 3.4), BiocParallel, SingleCellExperiment
Imports SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats, methods, utils, graphics, grDevices, Matrix, scater, edgeR, limma, dynamicTreeCut, FNN, igraph, shiny, zoo, statmod, splines, ggplot2, MASS, DT, viridis
LinkingTo beachmat, Rcpp, Rhdf5lib
Suggests testthat, BiocStyle, knitr, beachmat, HDF5Array, limSolve, org.Mm.eg.db, DESeq2, monocle, Rtsne, pracma, Biobase, irlba
SystemRequirements C++11
Enhances
URL
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_1.5.12.tar.gz
Windows Binary scran_1.5.12.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) scran_1.5.12.tgz
Source Repository git clone https://git.bioconductor.org/packages/scran
Package Short Url http://bioconductor.org/packages/scran/
Package Downloads Report Download Stats

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