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Dino

Normalization of Single-Cell mRNA Sequencing Data


Bioconductor version: Release (3.18)

Dino normalizes single-cell, mRNA sequencing data to correct for technical variation, particularly sequencing depth, prior to downstream analysis. The approach produces a matrix of corrected expression for which the dependency between sequencing depth and the full distribution of normalized expression; many existing methods aim to remove only the dependency between sequencing depth and the mean of the normalized expression. This is particuarly useful in the context of highly sparse datasets such as those produced by 10X genomics and other uninque molecular identifier (UMI) based microfluidics protocols for which the depth-dependent proportion of zeros in the raw expression data can otherwise present a challenge.

Author: Jared Brown [aut, cre] , Christina Kendziorski [ctb]

Maintainer: Jared Brown <brownj at ds.dfci.harvard.edu>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Dino")

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("Dino")
Normalization by distributional resampling of high throughput single-cell RNA-sequencing data HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CellBasedAssays, GeneExpression, Normalization, RNASeq, Regression, Sequencing, SingleCell, Software, Transcriptomics
Version 1.8.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL-3
Depends R (>= 4.0.0)
Imports BiocParallel, BiocSingular, SummarizedExperiment, SingleCellExperiment, S4Vectors, Matrix, Seurat, matrixStats, parallel, scran, grDevices, stats, methods
System Requirements
URL https://github.com/JBrownBiostat/Dino
Bug Reports https://github.com/JBrownBiostat/Dino/issues
See More
Suggests testthat (>= 2.1.0), knitr, rmarkdown, BiocStyle, devtools, ggplot2, gridExtra, ggpubr, grid, magick, hexbin
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package Dino_1.8.0.tar.gz
Windows Binary Dino_1.8.0.zip (64-bit only)
macOS Binary (x86_64) Dino_1.8.0.tgz
macOS Binary (arm64) Dino_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Dino
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Dino
Bioc Package Browser https://code.bioconductor.org/browse/Dino/
Package Short Url https://bioconductor.org/packages/Dino/
Package Downloads Report Download Stats