scran

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 wehi.edu.au>

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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scran")

 

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

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) (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, org.Mm.eg.db, DESeq2, monocle, pracma, Biobase, irlba, aroma.light
SystemRequirements	C++11
Enhances
URL
Depends On Me	simpleSingleCell
Imports Me	BASiCS, scDD
Suggests Me	scone, splatter
Links To Me
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
Package Short Url	http://bioconductor.org/packages/scran/
Package Downloads Report	Download Stats