This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see scran.
Bioconductor version: 3.8
Implements functions for low-level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell-specific biases, assignment of cell cycle phase, detection of highly variable and significantly correlated genes, correction of batch effects, identification of marker genes, and other common tasks in single-cell analysis workflows.
Author: Aaron Lun [aut, cre], Karsten Bach [aut], Jong Kyoung Kim [ctb], Antonio Scialdone [ctb], Laleh Haghverdi [ctb]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
Citation (from within R,
enter citation("scran")
):
To install this package, start R (version "3.5") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("scran")
For older versions of R, please refer to the appropriate Bioconductor release.
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 |
Reference Manual | ||
Text | NEWS |
biocViews | BatchEffect, Clustering, GeneExpression, ImmunoOncology, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization |
Version | 1.10.2 |
In Bioconductor since | BioC 3.3 (R-3.3) (3 years) |
License | GPL-3 |
Depends | R (>= 3.5), BiocParallel, SingleCellExperiment |
Imports | SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp (>= 0.12.14), stats, methods, utils, Matrix, scater, edgeR, limma, dynamicTreeCut, BiocNeighbors, igraph, statmod, DelayedArray, DelayedMatrixStats |
LinkingTo | beachmat, Rcpp, Rhdf5lib |
Suggests | testthat, BiocStyle, knitr, beachmat, HDF5Array, irlba, org.Mm.eg.db, DESeq2, monocle, pracma, Biobase, aroma.light |
SystemRequirements | C++11 |
Enhances | |
URL | |
Depends On Me | simpleSingleCell |
Imports Me | BASiCS, scDD |
Suggests Me | CellTrails, clusterExperiment, scone, splatter, TabulaMurisData |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | scran_1.10.2.tar.gz |
Windows Binary | scran_1.10.2.zip (32- & 64-bit) |
Mac OS X 10.11 (El Capitan) | scran_1.10.2.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 | http://bioconductor.org/packages/scran/ |
Package Downloads Report | Download Stats |
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