Dino

DOI: 10.18129/B9.bioc.Dino  

Normalization of Single-Cell mRNA Sequencing Data

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	CellBasedAssays, GeneExpression, Normalization, RNASeq, Regression, Sequencing, SingleCell, Software, Transcriptomics
Version	1.4.0
In Bioconductor since	BioC 3.14 (R-4.1) (1.5 years)
License	GPL-3
Depends	R (>= 4.0.0)
Imports	BiocParallel, BiocSingular, SummarizedExperiment, SingleCellExperiment, S4Vectors, Matrix, Seurat, matrixStats, parallel, scran, grDevices, stats, methods
LinkingTo
Suggests	testthat (>= 2.1.0), knitr, rmarkdown, BiocStyle, devtools, ggplot2, gridExtra, ggpubr, grid, magick, hexbin
SystemRequirements
Enhances
URL	https://github.com/JBrownBiostat/Dino
BugReports	https://github.com/JBrownBiostat/Dino/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	Dino_1.4.0.tar.gz
Windows Binary	Dino_1.4.0.zip
macOS Binary (x86_64)	Dino_1.4.0.tgz
macOS Binary (arm64)	Dino_1.4.0.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