MatrixQCvis

DOI: 10.18129/B9.bioc.MatrixQCvis    

Shiny-based interactive data-quality exploration for omics data

Bioconductor version: Release (3.15)

Data quality assessment is an integral part of preparatory data analysis to ensure sound biological information retrieval. We present here the MatrixQCvis package, which provides shiny-based interactive visualization of data quality metrics at the per-sample and per-feature level. It is broadly applicable to quantitative omics data types that come in matrix-like format (features x samples). It enables the detection of low-quality samples, drifts, outliers and batch effects in data sets. Visualizations include amongst others bar- and violin plots of the (count/intensity) values, mean vs standard deviation plots, MA plots, empirical cumulative distribution function (ECDF) plots, visualizations of the distances between samples, and multiple types of dimension reduction plots. Furthermore, MatrixQCvis allows for differential expression analysis based on the limma (moderated t-tests) and proDA (Wald tests) packages. MatrixQCvis builds upon the popular Bioconductor SummarizedExperiment S4 class and enables thus the facile integration into existing workflows. The package is especially tailored towards metabolomics and proteomics mass spectrometry data, but also allows to assess the data quality of other data types that can be represented in a SummarizedExperiment object.

Author: Thomas Naake [aut, cre] , Wolfgang Huber [aut]

Maintainer: Thomas Naake <thomasnaake at googlemail.com>

Installation

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

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

BiocManager::install("MatrixQCvis")

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("MatrixQCvis")

 

HTML	R Script	Shiny-based interactive data quality exploration of omics data
PDF		Reference Manual
Text		NEWS

Details

biocViews	DimensionReduction, GUI, Metabolomics, Proteomics, Software, Visualization
Version	1.4.0
In Bioconductor since	BioC 3.13 (R-4.1) (1.5 years)
License	GPL (>= 3)
Depends	SummarizedExperiment(>= 1.20.0), plotly (>= 4.9.3), shiny (>= 1.6.0)
Imports	ComplexHeatmap(>= 2.7.9), dplyr (>= 1.0.5), ggplot2 (>= 3.3.3), grDevices (>= 4.1.0), Hmisc (>= 4.5-0), htmlwidgets (>= 1.5.3), impute(>= 1.65.0), imputeLCMD (>= 2.0), limma(>= 3.47.12), methods (>= 4.1.0), openxlsx (>= 4.2.3), pcaMethods(>= 1.83.0), proDA(>= 1.5.0), rlang (>= 0.4.10), rmarkdown (>= 2.7), Rtsne (>= 0.15), S4Vectors(>= 0.29.15), shinydashboard (>= 0.7.1), shinyhelper (>= 0.3.2), shinyjs (>= 2.0.0), stats (>= 4.1.0), tibble (>= 3.1.1), tidyr (>= 1.1.3), umap (>= 0.2.7.0), UpSetR (>= 1.4.0), vegan (>= 2.5-7), vsn(>= 3.59.1)
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Suggests	BiocGenerics(>= 0.37.4), BiocStyle(>= 2.19.2), hexbin (>= 1.28.2), knitr (>= 1.33), testthat (>= 3.0.2)
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Build Report

Package Archives

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

Source Package	MatrixQCvis_1.4.0.tar.gz
Windows Binary	MatrixQCvis_1.4.0.zip
macOS Binary (x86_64)	MatrixQCvis_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MatrixQCvis
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MatrixQCvis
Package Short Url	https://bioconductor.org/packages/MatrixQCvis/
Package Downloads Report	Download Stats