scran

DOI: 10.18129/B9.bioc.scran    

Methods for Single-Cell RNA-Seq Data Analysis

Bioconductor version: Release (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>

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

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("scran", version = "3.8")

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, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.10.1
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, 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_1.10.1.tar.gz
Windows Binary scran_1.10.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) scran_1.10.1.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
Old Source Packages for BioC 3.8 Source Archive

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