DOI: 10.18129/B9.bioc.scran  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see scran.

Methods for Single-Cell RNA-Seq Data Analysis

Bioconductor version: 3.16

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>

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HTML R Script Using scran to analyze scRNA-seq data
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biocViews Clustering, GeneExpression, ImmunoOncology, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.26.2
In Bioconductor since BioC 3.3 (R-3.3) (7 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
Depends On Me OSCA.advanced, OSCA.basic, OSCA.intro, OSCA.multisample, OSCA.workflows, SingleRBook
Imports Me BASiCS, BASiCStan, BayesSpace, BioTIP, celda, ChromSCape, CiteFuse, conclus, Dino, FLAMES, IRISFGM, msImpute, mumosa, pipeComp, scDblFinder, scDD, 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
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