scran

DOI:10.18129/B9.bioc.scran

This is thedevelopmentversion of scran; for the stable release version, seescran.

Methods for Single-Cell RNA-Seq Data Analysis

Bioconductor version: Development (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

Installation

To install this package, start R (version "4.2") 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 appropriateBioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scran")

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

Details

biocViews	Clustering,GeneExpression,ImmunoOncology,Normalization,RNASeq,Sequencing,SingleCell,Software,Transcriptomics
Version	1.25.0
In Bioconductor since	BioC 3.3 (R-3.3) (6 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
Enhances
URL
Depends On Me	OSCA.advanced, OSCA.intro, OSCA.multisample, OSCA.workflows
Imports Me	BASiCS,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
Links To Me
Build Report

Package Archives

Followbob 体育网址 指示在R会话中使用这个包.

Source Package	scran_1.25.0.tar.gz
Windows Binary	scran_1.25.0.zip
macOS 10.13 (High Sierra)	scran_1.25.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scran
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scran
Package Short Url	//www.anjoumacpherson.com/packages/scran/
Package Downloads Report	Download Stats