scran
This is the development version of scran; for the stable release version, see scran.
Methods for Single-Cell RNA-Seq Data Analysis
Bioconductor version: Development (3.23)
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 "4.6") 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 appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Clustering, GeneExpression, ImmunoOncology, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.39.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (9.5 years) |
| License | GPL-3 |
| Depends | SingleCellExperiment, scuttle |
| Imports | SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, edgeR, limma, igraph, statmod, MatrixGenerics, S4Arrays, DelayedArray, BiocSingular, bluster, metapod, dqrng, beachmat |
| System Requirements | C++11 |
| URL | https://github.com/MarioniLab/scran/ |
| Bug Reports | https://github.com/MarioniLab/scran/issues |
See More
| Suggests | testthat, BiocStyle, knitr, rmarkdown, DelayedMatrixStats, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, pheatmap, scater |
| Linking To | Rcpp, beachmat, BH, dqrng, scuttle |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 | https://bioconductor.org/packages/scran/ |
| Package Downloads Report | Download Stats |