Dino

DOI: 10.18129/B9.bioc.Dino    

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

Normalization of Single-Cell mRNA Sequencing Data

Bioconductor version: Development (3.14)

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 biostat.wisc.edu>

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

Installation

To install this package, start R (version "4.1") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 0.99.11
In Bioconductor since BioC 3.14 (R-4.1)
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
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_0.99.11.tar.gz
Windows Binary Dino_0.99.11.zip
macOS 10.13 (High Sierra) Dino_0.99.11.tgz
Source Repository git clone https://git.bioconductor.org/packages/Dino
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Dino
Package Short Url https://bioconductor.org/packages/Dino/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: