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Bioconductor - scran

scran

This is the released version of scran; for the devel version, see scran.

Methods for Single-Cell RNA-Seq Data Analysis

Bioconductor version: Release (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")

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")

Details biocViews Clustering, GeneExpression, ImmunoOncology, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics Version 1.36.0 In Bioconductor since BioC 3.3 (R-3.3) (9 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 See More 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.advanced, OSCA.basic, OSCA.intro, OSCA.multisample, OSCA.workflows, SingleRBook Imports Me BASiCS, BASiCStan, BatchQC, BayesSpace, BioTIP, celda, chevreulPlot, chevreulProcess, ChromSCape, CiteFuse, DeconvoBuddies, Dino, epiregulon, epiregulon.extra, FLAMES, lute, MOSim, MPAC, msImpute, mumosa, pipeComp, scDblFinder, scDD, scMerge, scTreeViz, SingleCellSignalR, singleCellTK, Spaniel, SpaNorm, mixhvg, SpatialDDLS Suggests Me APL, Banksy, batchelor, bluster, CellTrails, clusterExperiment, decontX, destiny, dittoSeq, escape, escheR, ExperimentSubset, ggsc, ggspavis, Glimma, glmGamPoi, iSEEu, jazzPanda, miloR, Nebulosa, nnSVG, PCAtools, raer, ReactomeGSA, scDiagnostics, scDotPlot, schex, scone, scuttle, SingleCellAlleleExperiment, sketchR, smoothclust, spatialHeatmap, splatter, SPOTlight, StabMap, SVP, tidySingleCellExperiment, 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.

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