readme.Rmd

---
output: github_document
bibliography: references.bib
link-citations: true
nocite: |
  @peschel2020netcomi
---

```{r setup, echo = FALSE}
knitr::opts_chunk$set(fig.path="man/figures/readme/")
```

# NetCoMi <img src="man/figures/logo.png" align="right" height="200" />

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NetCoMi (**Net**work **Co**nstruction and Comparison for **Mi**crobiome Data) 
is an R package designed to facilitate the construction, analysis, and comparison of networks tailored to microbial compositional data. It implements a comprehensive workflow introduced in [Peschel et al. (2020)](https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbaa290/6017455), which guides users through each step of network generation and analysis with a strong emphasis on reproducibility and computational efficiency.

With NetCoMi, users can construct microbial association or dissimilarity networks directly from sequencing data, typically provided as a read count matrix. The package includes a broad selection of methods for handling zeros, normalizing data, computing associations between microbial taxa, and sparsifying the resulting matrices. By offering these components in a modular format, NetCoMi allows users to tailor the workflow to their specific research needs, creating highly customizable microbial networks.

The package supports both the construction, analysis, and visualization of a **single network** and the **comparison of two networks** through graphical and quantitative approaches, including statistical testing. Additionally, NetCoMi offers the capability of constructing **differential networks**, where only differentially associated taxa are connected.

<img src="man/figures/soilrep_networks.png" width=100% />

> Exemplary network comparison using soil microbiome data (['soilrep' data from 
phyloseq package](https://github.com/joey711/phyloseq/blob/master/data/soilrep.RData)). 
Microbial associations are compared between the two experimantal settings 
'warming' and 'non-warming' using the same layout in both groups. 

## Website

Please visit [netcomi.de](https://netcomi.de/) for a complete reference.

## Installation

```{r install, eval=FALSE}
# Required packages
install.packages("devtools")
install.packages("BiocManager")

# Since two of NetCoMi's dependencies are only available on GitHub, 
# it is recommended to install them first:
devtools::install_github("zdk123/SpiecEasi")
devtools::install_github("GraceYoon/SPRING")

# Install NetCoMi
devtools::install_github("stefpeschel/NetCoMi", 
                         repos = c("https://cloud.r-project.org/",
                                   BiocManager::repositories()))
```

If there are any errors during installation, please install the missing 
dependencies manually.

Packages that are optionally required in certain settings are not installed 
together with NetCoMi. These can be installed automatically using:

```{r install2, eval=FALSE}
installNetCoMiPacks()
```

If not installed via `installNetCoMiPacks()`, the required package is installed
by the respective NetCoMi function when needed.

## Bioconda

Thanks to [daydream-boost](https://github.com/daydream-boost), NetCoMi can also
be installed from conda bioconda channel with

```bash
# You can install an individual environment firstly with
# conda create -n NetCoMi
# conda activate NetCoMi
conda install -c bioconda -c conda-forge r-netcomi
```

## Development version

Everyone who wants to use new features not included in any releases 
is invited to install NetCoMi's development version:

```{r install4, eval=FALSE}
devtools::install_github("stefpeschel/NetCoMi", 
                         ref = "develop",
                         repos = c("https://cloud.r-project.org/",
                                   BiocManager::repositories()))
```

Please check the [NEWS](https://github.com/stefpeschel/NetCoMi/blob/develop/NEWS.md) 
document for features implemented on develop branch.


## References