scran

DOI: 10.18129/B9.bioc.scran    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see scran.

Methods for Single-Cell RNA-Seq Data Analysis

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

HTML	R Script	Using scran to analyze scRNA-seq data
PDF		Reference Manual
Text		NEWS

Details

biocViews	BatchEffect, Clustering, GeneExpression, ImmunoOncology, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version	1.10.2
In Bioconductor since	BioC 3.3 (R-3.3) (3 years)
License	GPL-3
Depends	R (>= 3.5), BiocParallel, SingleCellExperiment
Imports	SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp (>= 0.12.14), stats, methods, utils, Matrix, scater, edgeR, limma, dynamicTreeCut, BiocNeighbors, igraph, statmod, DelayedArray, DelayedMatrixStats
LinkingTo	beachmat, Rcpp, Rhdf5lib
Suggests	testthat, BiocStyle, knitr, beachmat, HDF5Array, irlba, org.Mm.eg.db, DESeq2, monocle, pracma, Biobase, aroma.light
SystemRequirements	C++11
Enhances
URL
Depends On Me	simpleSingleCell
Imports Me	BASiCS, scDD
Suggests Me	CellTrails, clusterExperiment, scone, splatter, TabulaMurisData
Links To Me
Build Report

Package Archives

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

Source Package	scran_1.10.2.tar.gz
Windows Binary	scran_1.10.2.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	scran_1.10.2.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