README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# DivComAnalyses

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The goal of DivComAnalyses is to facilitate community analysis (e.g., 16S community metabarcoding, metaphlan taxonomic profiling from metagenomes). In data filtering (i.e., potential contaminants identified using decontam R package), in normalizing data (i.e., 16S qPCR normalization), generate phylogenetic and taxonomic alpha and beta-diversity metrics, visualize community composition and structure using unconstrained and constrained ordination, facilitate statistical analysis based on DEseq2, ALDex2, vegan R packages.

## Tutorial

You can find the latest version of the tutorial [here](http://htmlpreview.github.io/?https://github.com/fconstancias/DivComAnalyses/blob/master/SOP/community_analyses/Microbiome_R_tutorial.html).


## Installation

You can't install the package  from [GitHub](https://github.com/) yet. You will need to source the `R` files where the functions are defined - see Tutorial.

``` r
## install.packages("devtools")
#devtools::install_github("fconstancias/DivComAnalyses")
```