scran
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see scran.
Methods for Single-Cell RNA-Seq Data Analysis
Bioconductor version: 3.7
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 <alun at wehi.edu.au>
citation("scran")):
Installation
To install this package, start R (version "3.5") 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 perform basic analyses of single-cell RNA-seq data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, Clustering, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization |
| Version | 1.8.4 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 years) |
| License | GPL-3 |
| Depends | R (>= 3.5), BiocParallel, SingleCellExperiment |
| Imports | SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp (>= 0.12.14), stats, methods, utils, graphics, grDevices, Matrix, scater, edgeR, limma, dynamicTreeCut, FNN, igraph, shiny, statmod, ggplot2, DT, viridis, DelayedArray, DelayedMatrixStats |
| System Requirements | C++11 |
| URL |
See More
| Suggests | testthat, BiocStyle, knitr, beachmat, HDF5Array, limSolve, org.Mm.eg.db, DESeq2, monocle, pracma, Biobase, irlba, aroma.light |
| Linking To | beachmat, Rcpp, Rhdf5lib |
| Enhances | |
| Depends On Me | simpleSingleCell |
| Imports Me | BASiCS, scDD |
| Suggests Me | scone, splatter |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scran_1.8.4.tar.gz |
| Windows Binary | scran_1.8.4.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | scran_1.8.4.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 3.7 | Source Archive |