DOI: 10.18129/B9.bioc.scran    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see scran.

Methods for Single-Cell RNA-Seq Data Analysis

Bioconductor version: 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>

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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 1.14.6
In Bioconductor since BioC 3.3 (R-3.3) (4 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, scRNAseq, dynamicTreeCut, DESeq2, monocle, Biobase, aroma.light, pheatmap
SystemRequirements C++11
Depends On Me
Imports Me BASiCS, scDblFinder, scDD
Suggests Me batchelor, CellTrails, clusterExperiment, fcoex, HCAData, PCAtools, schex, scone, simpleSingleCell, SingleR, splatter, TabulaMurisData
Links To Me
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