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 (3.21)

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>

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Clustering, GeneExpression, ImmunoOncology, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.35.0
In Bioconductor since	BioC 3.3 (R-3.3) (8.5 years)
License	GPL-3
Depends	SingleCellExperiment, scuttle
Imports	SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, edgeR, limma, igraph, statmod, MatrixGenerics, S4Arrays, DelayedArray, BiocSingular, bluster, metapod, dqrng, beachmat
System Requirements	C++11
URL	https://github.com/MarioniLab/scran/
Bug Reports	https://github.com/MarioniLab/scran/issues

Suggests	testthat, BiocStyle, knitr, rmarkdown, DelayedMatrixStats, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, pheatmap, scater
Linking To	Rcpp, beachmat, BH, dqrng, scuttle
Enhances
Depends On Me	OSCA.intro, OSCA.workflows, SingleRBook
Imports Me	BASiCS, BASiCStan, BatchQC, BayesSpace, BioTIP, ChromSCape, CiteFuse, Dino, FLAMES, MOSim, MPAC, SingleCellSignalR, SpaNorm, Spaniel, celda, epiregulon.extra, epiregulon, lute, msImpute, mumosa, pipeComp, scDD, scDblFinder, scMerge, scTreeViz, singleCellTK, mixhvg, SC.MEB, SpatialDDLS
Suggests Me	Banksy, CellTrails, ExperimentSubset, Glimma, Nebulosa, PCAtools, SPOTlight, SingleCellAlleleExperiment, SingleR, StabMap, TSCAN, batchelor, bluster, clusterExperiment, decontX, dittoSeq, escape, escheR, ggsc, ggspavis, glmGamPoi, iSEEu, miloR, nnSVG, raer, scDiagnostics, scDotPlot, schex, scone, scuttle, sketchR, smoothclust, spatialHeatmap, splatter, tidySingleCellExperiment, tpSVG, transformGamPoi, velociraptor, HCAData, SingleCellMultiModal, TabulaMurisData, simpleSingleCell, Canek, SCdeconR
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	scran_1.35.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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