alxeleratoR easy phyloseq data analysis Public R package to accelerate data analysis, so you can focus on interpretation during data exploration instead of finding out how to code your question to ask to `phyloseq` objects. This "package"/bundle evolved from my own need to automate and share common analyses and visualizations. Most functions require `phyloseq` or similar data structures. Many functions are wrappers around, or drop-in replacements of, existing functions or packages. Some functions are original creations while others are "borrowed" and adapted to my personal needs (*I tried giving credits as appropriate as possible. If you think I’ve forgotten to credit you, please drop me a message*). The primary context of my work is microbiome, resistome, metagenomics, and eDNA research. But feel free to use them in different contexts. Make sure to read the disclaimer and double check if functions are fit for its purpose. Outcomes could be erroneous!. This package/repository is maintained by: Alex Bossers (creator) One Health Microbial Group, Institute for Risk Assessment Sciences, Utrecht University, NL PathogenOmics and Bioinformatics Group, Wageningen BioVeterinary Research, NL Peter Scherpenisse One Health Microbial Group, Institute for Risk Assessment Sciences, Utrecht University, NL Any additions or bug fixes are more than welcome! Examples of use Checkout our github wiki page here: github.com/alxelerator/alxeleratoR/wiki to see some features in action! Disclaimer This package are primarily tailored to my own needs and may be subject to changes. While I will strive to ensure backward compatibility, this is not guaranteed (including preservation of defaults). The use of these functions is entirely at your own risk. You should always validate the outcomes, as they may contain errors or inaccuracies. Neither I, any collaborators, nor the associated institutions can be held liable for any direct or indirect damage caused by the use of this package. Proceed with caution and ensure thorough validation when using or integrating this package into your workflow! Installation In R run `devtools::install_github("alxelerator/alxeleratoR")` After loading the package `library(alxeleratoR)` you can set some convenient defaults using `alxinit()` If you need to install some missing packages I can strongly recommend the use of BioConductor package management. Install it using `install.packages("BiocManager")` or update using `BiocManager::install()` For instance these packages are required for the full experience `BiocManager::install(c("tidyverse", "phyloseq", "pals", "cowplot", "RColorBrewer", "foreach", "openssl", "Biostrings", "rstatix", "scales", "vegan"))` Documentation Function details are covered by each function's documentation. Credits Credits go to the individual original authors of a few scavenged but changed functions (see the details of these functions). License This project is licensed under the [GNU General Public License](https://www.gnu.org/licenses/gpl-3.0.html). You are free to use, modify, and distribute this package as long as you adhere to the terms of the license.