scran

Methods for Single-Cell RNA-Seq Data Analysis

Bioconductor version: 3.23 · Package version: 1.40.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scran")

Details

Maintainer	Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Author	Aaron Lun [aut, cre], Karsten Bach [aut], Jong Kyoung Kim [ctb], Antonio Scialdone [ctb]
License	GPL-3
URL	https://github.com/MarioniLab/scran/
Bug Reports	https://github.com/MarioniLab/scran/issues
System Requirements	C++11
Downloads rank	8027
Source branch	RELEASE_3_23
biocViews	Clustering, GeneExpression, ImmunoOncology, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics

Documentation

Using scran to analyze single-cell RNA-seq data

Download

Source package

Dependencies

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

LinkingTo: Rcpp, beachmat, BH, dqrng, scuttle

Suggests: testthat, BiocStyle, knitr, rmarkdown, DelayedMatrixStats, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, pheatmap, scater, scrapper

Reverse dependencies

Imports Me (32): BASiCS, BASiCStan, BatchQC, BayesSpace, BioTIP, celda, chevreulPlot, chevreulProcess, ChromSCape, CiteFuse, Coralysis, DeconvoBuddies, Dino, epiregulon, epiregulon.extra, FLAMES, mixhvg, MOSim, MPAC, msImpute, mumosa, pipeComp, scDblFinder, scDD, scMerge, scTreeViz, scTypeEval, singIST, singleCellTK, Spaniel, SpaNorm, StatescopeR

Suggests Me (55): anglemania, APL, Banksy, batchelor, blase, bluster, Canek, CellTrails, clusterExperiment, decontX, destiny, dittoSeq, DOtools, escape, escheR, ExperimentSubset, ggsc, ggspavis, Glimma, glmGamPoi, HCAData, immLynx, iSEEu, jazzPanda, miloR, Nebulosa, nnSVG, PCAtools, raer, ReactomeGSA, scConform, scDiagnostics, scDotPlot, schex, scLANE, scone, scuttle, simPIC, simpleSingleCell, SingleCellAlleleExperiment, SingleCellMultiModal, sketchR, smoothclust, splatter, SPOTlight, StabMap, SuperCellCyto, SVP, TabulaMurisData, tidySingleCellExperiment, tpSVG, transformGamPoi, TSCAN, velociraptor, Voyager