scran
Methods for Single-Cell RNA-Seq Data Analysis
Bioconductor version: Release (3.17)
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("scran")):
Installation
To install this package, start R (version "4.3") 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")| Using scran to analyze scRNA-seq data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, GeneExpression, ImmunoOncology, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.28.2 |
| In Bioconductor since | BioC 3.3 (R-3.3) (7.5 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 |
| Linking To | Rcpp, beachmat, BH, dqrng, scuttle |
| Suggests | testthat, BiocStyle, knitr, rmarkdown, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, monocle, Biobase, pheatmap, scater |
| System Requirements | C++11 |
| Enhances | |
| URL |
See More
| Depends On Me | OSCA.advanced, OSCA.basic, OSCA.intro, OSCA.multisample, OSCA.workflows, SingleRBook |
| Imports Me | BASiCS, BASiCStan, BayesSpace, BioTIP, celda, ChromSCape, CiteFuse, Dino, FLAMES, IRISFGM, msImpute, mumosa, pipeComp, scDblFinder, scDD, scMerge, 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 |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scran_1.28.2.tar.gz |
| Windows Binary | scran_1.28.2.zip |
| macOS Binary (x86_64) | scran_1.28.2.tgz |
| macOS Binary (arm64) | scran_1.28.2.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 |
| Old Source Packages for BioC 3.17 | Source Archive |