zitools

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

Analysis of zero-inflated count data


Bioconductor version: Development (3.20)

zitools allows for zero inflated count data analysis by either using down-weighting of excess zeros or by replacing an appropriate proportion of excess zeros with NA. Through overloading frequently used statistical functions (such as mean, median, standard deviation), plotting functions (such as boxplots or heatmap) or differential abundance tests, it allows a wide range of downstream analyses for zero-inflated data in a less biased manner. This becomes applicable in the context of microbiome analyses, where the data is often overdispersed and zero-inflated, therefore making data analysis extremly challenging.

Author: Carlotta Meyring [aut, cre]

Maintainer: Carlotta Meyring <carlotta.meyring at uniklinik-freiburg.de>

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

Installation

To install this package, start R (version "4.4") and enter:


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

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

BiocManager::install("zitools")

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("zitools")
An Introduction to zitools PDF R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Microbiome, Software, StatisticalMethod
Version 0.99.5
In Bioconductor since BioC 3.20 (R-4.4)
License BSD_3_clause + file LICENSE
Depends R (>= 4.4.0), methods
Imports phyloseq, pscl, ggplot2, MatrixGenerics, SummarizedExperiment, stats, VGAM, matrixStats, tidyr, tibble, dplyr, DESeq2, reshape2, RColorBrewer, magrittr, BiocGenerics, graphics, utils
System Requirements
URL https://github.com/kreutz-lab/zitools
Bug Reports https://github.com/kreutz-lab/zitools/issues
See More
Suggests knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), tidyverse, microbiome
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Package Archives

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

Source Package zitools_0.99.5.tar.gz
Windows Binary zitools_0.99.5.zip
macOS Binary (x86_64) zitools_0.99.5.tgz
macOS Binary (arm64) zitools_0.99.5.tgz
Source Repository git clone https://git.bioconductor.org/packages/zitools
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/zitools
Bioc Package Browser https://code.bioconductor.org/browse/zitools/
Package Short Url https://bioconductor.org/packages/zitools/
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