scran

DOI: 10.18129/B9.bioc.scran  

Methods for Single-Cell RNA-Seq Data Analysis

Bioconductor version: Release (3.17)

Implements miscellaneous functions for interpretation of single-cell RNA-seq data. Methods are provided for 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>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("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	Clustering, GeneExpression, ImmunoOncology, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.28.2
In Bioconductor since	BioC 3.3 (R-3.3) (7.5 years)
License	GPL-3
Depends	SingleCellExperiment, scuttle
Imports	SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, edgeR, limma, igraph, statmod, DelayedArray, DelayedMatrixStats, BiocSingular, bluster, metapod, dqrng, beachmat
LinkingTo	Rcpp, beachmat, BH, dqrng, scuttle
Suggests	testthat, BiocStyle, knitr, rmarkdown, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, monocle, Biobase, pheatmap, scater
SystemRequirements	C++11
Enhances
URL
Depends On Me	OSCA.advanced, OSCA.basic, OSCA.intro, OSCA.multisample, OSCA.workflows, SingleRBook
Imports Me	BASiCS, BASiCStan, BayesSpace, BioTIP, celda, ChromSCape, CiteFuse, Dino, FLAMES, IRISFGM, msImpute, mumosa, pipeComp, scDblFinder, scDD, scMerge, scTreeViz, SingleCellSignalR, singleCellTK, Spaniel, spatialHeatmap
Suggests Me	APL, batchelor, bluster, CellTrails, clusterExperiment, destiny, dittoSeq, ExperimentSubset, fcoex, ggspavis, Glimma, glmGamPoi, HCAData, iSEEu, miloR, Nebulosa, nnSVG, PCAtools, schex, scone, scuttle, simpleSingleCell, SingleCellMultiModal, SingleR, splatter, SPOTlight, TabulaMurisData, tidySingleCellExperiment, transformGamPoi, TSCAN, velociraptor, Voyager
Links To Me
Build Report

Package Archives

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

Source Package	scran_1.28.2.tar.gz
Windows Binary	scran_1.28.2.zip
macOS Binary (x86_64)	scran_1.28.2.tgz
macOS Binary (arm64)	scran_1.28.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scran
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scran
Bioc Package Browser	https://code.bioconductor.org/browse/scran/
Package Short Url	https://bioconductor.org/packages/scran/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive