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 (3.11)

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, identification of marker genes, and other common tasks in routine single-cell analysis workflows.

Author: Aaron Lun [aut, cre], Karsten Bach [aut], Jong Kyoung Kim [ctb], Antonio Scialdone [ctb]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.15.9
In Bioconductor since BioC 3.3 (R-3.3) (3.5 years)
License GPL-3
Depends SingleCellExperiment
Imports SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, scater, edgeR, limma, BiocNeighbors, igraph, statmod, DelayedArray, DelayedMatrixStats, BiocSingular, dqrng
LinkingTo Rcpp, beachmat, BH, dqrng
Suggests testthat, BiocStyle, knitr, beachmat, HDF5Array, scRNAseq, dynamicTreeCut, DESeq2, monocle, Biobase, pheatmap
SystemRequirements C++11
Enhances
URL
Depends On Me
Imports Me BASiCS, scDblFinder, scDD
Suggests Me batchelor, CellTrails, clusterExperiment, fcoex, HCAData, PCAtools, schex, scone, simpleSingleCell, SingleR, splatter, TabulaMurisData
Links To Me
Build Report  

Package Archives

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

Source Package scran_1.15.9.tar.gz
Windows Binary scran_1.15.9.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) scran_1.15.9.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 https://bioconductor.org/packages/scran/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: