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https://github.com/ebedthan/corebiota

Probabilistic partition of count data to identify core species
https://github.com/ebedthan/corebiota

bioinformatics microbiome r

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Probabilistic partition of count data to identify core species

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# corebiota

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## Probabilistic core microbiota analysis

The goal of corebiota is to provide a set of functions to easily and robustly perform core microbiota analysis from an ASV/OTU table. It also put emphasis on robustness by providing a probabilistic framework and reproducibility.

The API is as follow:

- First, with the function [`sad`](https://ebedthan.github.io/corebiota/reference/sad.html) you can rapidly perform a species abundance distribution modeling following a Poisson distribution and identify microbes belonging to either core or satellite group in your community.

- You can also directly get the core microbiota through [`get_core`](https://ebedthan.github.io/corebiota/reference/get_core.html).

Miscellaneous functions, nonetheless important, are:

- [`plot_graph`](https://ebedthan.github.io/corebiota/reference/plot_graph.html) function which plot a nice graph showin the partition of you microbiome into satellite and core members.
- [`get_satellite`](https://ebedthan.github.io/corebiota/reference/get_satellite.html) which return the satellite members of your community.

Yes, all the function can take as input a phyloseq object.

This package have only phyloseq as an external dependcy for your joy. We therefore, extensively use R Base and only pheatmap, covr and usethis as suggests.

## Installation

You can install the development version of corebiota like so:

``` r
# Install devtools package (if not already done!)
install.package("remotes")

# Load devtools package
library(remotes)

# Install corebiota package
install_github("Ebedthan/corebiota")
```

## Example

This is a basic example which shows you how to solve a common problem:

``` r
library(corebiota)

# Some fake data
asv_tbl <- data.frame(sample1 = 1:10, sample2 = 10:1, sample3 = 80:89)
rownames(asv_tbl) <- paste0("ASV", "_", 1:10)

sad(asv_tbl)
```

Enjoy!

## Some great papers on designing a core microbiota analysis

- Neu, A.T., Allen, E.E., Roy, K., 2021. Defining and quantifying the core microbiome: Challenges and prospects. PNAS 118.
- Berg, G., Rybakova, D., Fischer, D. et al., 2020. Microbiome definition re-visited: old concepts and new challenges. Microbiome 8, 103.
- Astudillo‐García, C., Bell, J.J., Webster, N.S. et al., 2017. Evaluating the core microbiota in complex communities: A systematic investigation. Environ Microbiol 19, 1450–1462.