DOI: 10.18129/B9.bioc.scran    

This is the development version of scran; to use it, please install the devel version of Bioconductor.

Methods for Single-Cell RNA-Seq Data Analysis

Bioconductor version: Development (3.10)

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, 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>

Citation (from within R, enter citation("scran")):


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if (!requireNamespace("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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HTML R Script Using scran to analyze scRNA-seq data
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biocViews BatchEffect, Clustering, GeneExpression, ImmunoOncology, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.13.30
In Bioconductor since BioC 3.3 (R-3.3) (3.5 years)
License GPL-3
Depends SingleCellExperiment
Imports SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, scater, edgeR, limma, BiocNeighbors, igraph, statmod, DelayedArray, DelayedMatrixStats, BiocSingular, dqrng
LinkingTo Rcpp, beachmat, BH, dqrng
Suggests testthat, BiocStyle, knitr, beachmat, HDF5Array,, dynamicTreeCut, DESeq2, monocle, Biobase, aroma.light
SystemRequirements C++11
Depends On Me
Imports Me BASiCS, scDD
Suggests Me batchelor, CellTrails, clusterExperiment, HCAData, PCAtools, scone, simpleSingleCell, SingleR, splatter, TabulaMurisData
Links To Me
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Source Package scran_1.13.30.tar.gz
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Mac OS X 10.11 (El Capitan) scran_1.13.30.tgz
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