zitools
This is the development version of zitools; for the stable release version, see zitools.
Analysis of zero-inflated count data
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Carlotta Meyring <carlotta.meyring at uniklinik-freiburg.de>
citation("zitools")):
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("zitools")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Microbiome, Software, StatisticalMethod |
| Version | 1.1.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (< 6 months) |
| 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 |
| 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 | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/zitools |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/zitools |
| Package Short Url | https://bioconductor.org/packages/zitools/ |
| Package Downloads Report | Download Stats |