scran

DOI: 10.18129/B9.bioc.scran    

Methods for Single-Cell RNA-Seq Data Analysis

Bioconductor version: Release (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>

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	1.6.9
In Bioconductor since	BioC 3.3 (R-3.3) (2 years)
License	GPL-3
Depends	R (>= 3.4), BiocParallel, SingleCellExperiment
Imports	SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp (>= 0.12.14), stats, methods, utils, graphics, grDevices, Matrix, scater, edgeR, limma, dynamicTreeCut, FNN, igraph, shiny, zoo, statmod, ggplot2, DT, viridis
LinkingTo	beachmat, Rcpp, Rhdf5lib
Suggests	testthat, BiocStyle, knitr, beachmat, HDF5Array, limSolve, org.Mm.eg.db, DESeq2, monocle, Rtsne, pracma, Biobase, irlba, aroma.light
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_1.6.9.tar.gz
Windows Binary	scran_1.6.9.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	scran_1.6.9.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scran
Package Short Url	http://bioconductor.org/packages/scran/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive