README.Rmd

---
title: "Network Correlation Analysis (NECorr)"
output: github_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

# Contents

-   [Overview](#overview)
-   [Repo Contents](#repo-contents)
-   [System Requirements](#system-requirements)
-   [Installation Guide](#installation-guide)
-   [Instructions for Use](#instructions-for-use)
-   [License](./LICENSE)
-   [Citation](#citation)

# Overview {#overview}

NECorr is a R package based on multiple-criteria decision-making algorithms. With the objective of ranking genes and their interactions in a selected condition or tissue, NECorr uses molecular network topology as well as global transcriptomics analysis to find condition/tissue-specific hub genes and their regulators.

# Repo Contents {#repo-contents}

-   [R](./R): `R` package code.
-   [man](./man): package manual for help in R session.
-   [int](./data): test data using dummies datasets and model.
-   [tests](./tests): `R` test with the data.

# System Requirements {#system-requirements}

## Hardware Requirements

The package require a long running time depending of the size of molecular network. A computer with 16 GB RAM is recommended to run the package.
The necessary C++ or GCC libraries are needed as the software is running partially on Rccp.

## Software Requirements

### OS Requirements

This package is supported for *Mac OS*, *Windows* and *Linux* operating systems. The package has been tested on the following systems:

Linux: Redhat RHEL 7.4\
Mac OSX: OS X 11.2.3; and 12.6

The NECorr packages requires the R version 3.4.2 or higher and a standard computer with enough RAM to support the operations defined by a user. For minimal performance, this will be a computer with about 1 GB of RAM.

### Installing R version 3.5 on Linux

The latest version of R can be installed as follows on *Linux*:

```{bash eval=FALSE, include=TRUE}
wget https://cran.rstudio.com/bin/macosx/R-3.4.2.pkg
sudo installer -pkg R-3.5.2.pkg -target /

```

# Installation Guide {#installation-guide}

## Devtools
From an `R` session, type:

```{r eval=FALSE, include=TRUE}
require(devtools)
install_github('warelab/NECorr', build_vignettes=TRUE, dependencies=TRUE, upgrade_dependencies=TRUE)  
```

The package should take approximately 20 seconds to install with vignettes on a recommended computer.

## Package Versions

The `NECorr` package dependencies will be installed automatically. 
The following [BioConductor](https://www.bioconductor.org/) package will need to be installed separately

```{r eval=FALSE, include=TRUE}
Biobase: 2.54.0
BiocGenerics: 0.40.0
limma: 3.50.3 
AnnotationDbi: 1.56.2
GenomeInfoDbData: 1.2.7 
supraHex: 1.14.0
```

# Instructions for Use {#instructions-for-use}

Please see the vignettes for help using the package:

```{r eval=FALSE, include=TRUE}
vignette("Necorr", package="NECorr")
vignette("gini", package="NECorr")
```

# Citation {#citation}

For citing code or the paper, please use [this citation](https://www.biorxiv.org/content/early/2018/05/21/326868).