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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 (3.20)

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 "4.4") 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

Details

biocViews Clustering, GeneExpression, ImmunoOncology, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.33.0
In Bioconductor since BioC 3.3 (R-3.3) (8 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
System Requirements C++11
URL
See More
Suggests testthat, BiocStyle, knitr, rmarkdown, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, pheatmap, scater
Linking To Rcpp, beachmat, BH, dqrng, scuttle
Enhances
Depends On Me OSCA.basic, OSCA.intro, OSCA.multisample, OSCA.workflows
Imports Me BASiCS, BASiCStan, BatchQC, BayesSpace, celda, ChromSCape, CiteFuse, Dino, epiregulon, epiregulon.extra, FLAMES, lute, MOSim, msImpute, mumosa, pipeComp, scDblFinder, scDD, scMerge, scTreeViz, SingleCellSignalR, singleCellTK, Spaniel, spatialHeatmap, digitalDLSorteR, mixhvg, SC.MEB, SpatialDDLS
Suggests Me APL, Banksy, batchelor, bluster, CellTrails, clusterExperiment, decontX, destiny, dittoSeq, escape, escheR, ExperimentSubset, ggsc, ggspavis, Glimma, glmGamPoi, iSEEu, miloR, Nebulosa, nnSVG, PCAtools, raer, schex, scone, scuttle, SingleCellAlleleExperiment, SingleR, sketchR, smoothclust, splatter, SPOTlight, tidySingleCellExperiment, tidySpatialExperiment, tpSVG, transformGamPoi, TSCAN, velociraptor, Voyager, 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_1.33.0.tar.gz
Windows Binary scran_1.33.0.zip
macOS Binary (x86_64) scran_1.33.0.tgz
macOS Binary (arm64) scran_1.33.0.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