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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#"
)
```
# BioNERO <img src='man/figures/logo.png' align="right" height="139" />
<!-- badges: start -->
[](https://github.com/almeidasilvaf/BioNERO/issues)
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](https://github.com/almeidasilvaf/BioNERO/actions)
[](https://codecov.io/gh/almeidasilvaf/BioNERO?branch=devel)
<!-- badges: end -->
`BioNERO` aims to integrate all aspects of biological network inference
in a single package, so users don't have to learn the syntaxes of several
packages and how to communicate among them. `BioNERO` features:
- **Expression data preprocessing** using state-of-the-art techniques for
network inference.
- **Automated exploratory data analyses**, including principal component
analysis (PCA) and heatmaps of gene expression or sample correlations.
- **Inference of gene coexpression networks (GCNs)** using the popular WGCNA
algorithm.
- **Inference of gene regulatory networks (GRNs)** based on the "wisdom
of the crowds" principle. This principle consists in inferring GRNs with
multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating
the average rank for each interaction pair.
- **Exploration of network topology** of GCNs, GRNs, and protein-protein
interaction networks.
- **Network visualization**.
- **Network comparison**, including identification of consensus modules
across independent expression sets, and calculation of intra and interspecies
module preservation statistics between different networks.
## Installation instructions
Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `BioNERO` from [Bioconductor](http://bioconductor.org/) using the following code:
```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("BioNERO")
```
And the development version from [GitHub](https://github.com/almeidasilvaf/BioNERO) with:
```{r 'install_dev', eval = FALSE}
BiocManager::install("almeidasilvaf/BioNERO")
```
## Citation
Below is the citation output from using `citation('BioNERO')` in R. Please
run this yourself to check for any updates on how to cite __BioNERO__.
```{r 'citation', eval = requireNamespace('BioNERO')}
print(citation('BioNERO'), bibtex = TRUE)
```
Please note that the `BioNERO` was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.