Dino
This is the development version of Dino; for the stable release version, see Dino.
Normalization of Single-Cell mRNA Sequencing Data
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Jared Brown <brownj at ds.dfci.harvard.edu>
citation("Dino")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("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")| Normalization by distributional resampling of high throughput single-cell RNA-sequencing data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CellBasedAssays, GeneExpression, Normalization, RNASeq, Regression, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.13.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (3 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Dino_1.13.0.tar.gz |
| Windows Binary (x86_64) | Dino_1.13.0.zip |
| macOS Binary (x86_64) | Dino_1.13.0.tgz |
| macOS Binary (arm64) | |
| 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 |