zitools
Analysis of zero-inflated count data
Bioconductor version: 3.24 · Package version: 1.7.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("zitools")Details
| Maintainer | Carlotta Meyring <carlotta.meyring@uniklinik-freiburg.de> |
| Author | Carlotta Meyring [aut, cre] (ORCID: <https://orcid.org/0009-0000-6201-7615>) |
| License | BSD_3_clause + file LICENSE |
| URL | https://github.com/kreutz-lab/zitools |
| Bug Reports | https://github.com/kreutz-lab/zitools/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Microbiome, Software, StatisticalMethod |
| Package Short Url | https://bioconductor.org/packages/zitools/ |
Citation
From within R, enter citation("zitools"):
Carlotta Meyring. zitools: Analysis of zero-inflated count data. doi:10.18129/B9.bioc.zitools, R package version 1.7.0, https://bioconductor.org/packages/zitools.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | zitools_1.7.0.tar.gz |
| Windows binary (x86_64) | zitools_1.7.0.zip |
| macOS binary (arm64) | zitools_1.7.0.tgz |
| macOS binary (x86_64) | zitools_1.7.0.tgz |
Dependencies
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
Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), tidyverse, microbiome