ahmohamed / NetPathMiner

NetPathMiner: R package for network path mining through gene expression

NetPathMiner

NetPathMiner implements a flexible module-based process flow for network path mining and visualization, which can be fully integrated with user-customized functions. It supports construction of various types of genome scale networks from three different pathway file formats, enabling its utility to most common pathway databases. In addition, NetPathMiner provides different visualization techniques to facilitate the analysis of even thousands of output paths.

To report bugs and arising issues, please visit https://github.com/ahmohamed/NetPathMiner

Installation Instructions

Using Docker

You can use NetPathMiner in a containerized form by pulling the image from docker hub. This is the easiest way to automatically manage system dependencies. It currently the recommended way to use NetPathMiner on Windows.

docker pull ahmohamed/netpathminer
docker run -e PASSWORD=bioc -p 8787:8787 ahmohamed/netpathminer:latest

In your browser, navigate to RStudio will be available on your web browser at http://localhost:8787. The USER is fixed to always being rstudio. The password in the above command is given as bioc but it can be set to anything. For more information on how-to-use, refer to Bioconductor help page.

You can access your local files by mapping to the container:

docker run -e PASSWORD=bioc -p 8787:8787 \
  -v "path/to/data_folder":"/home/rstudio/data_folder" \
  ahmohamed/netpathminer:latest

You should see data_folder in your working directory.

System Prerequisites

If you are not using docker, you need to install system depedencies for NetPathMiner. NetPathMiner depends on libxml2 and libsbml to process pathway files. Installation or running certain functions MAY fail if these prerequisite libraries are not available. Please read through the following instructions.

Prerequisites for Unix users (Linux and Mac OS)

Installing libxml2

Make sure your system has library libxml2 installed. In Mac OSX 10.6 or later, libxml2 are built in. For Linux users also, this is almost always the case, however, developing headers may be missing. To install libxml2 and the headers:

    sudo apt-get install libxml2   
    sudo apt-get install libxml2-dev   

Installing libSBML

Installing libSBML for Unix users is optional. However, NetPathMiner will not be able to process SBML files. If you will not use SBML functions, you can skip this part.

From the website of libSBML http://sbml.org/Software/libSBML, you can directly download the binaries suitable for your system from Download libSBML link. You can follow the installation instructions on the website.

Prerequisites for Windows users

If you are installing the package through Bioconductor, you don't have to install external libraries. However, currently the Bioconductor version for Windows doesn't support SBML processing.

Docker installtion is currently the recommended way to use NetPathMiner on Windows.

Alternatively, we have prepared all dependencies in a tar file, downloadable from https://github.com/ahmohamed/NPM_dependencies . Please download the file and place in in the home directory of R (type R RHOME in command prompt to locate it), before installation.

Unless you want to use customized libraries, you can skip the rest of this section.To use customized libraries, you have to compile them and provide them to R at the time of installation. This is not a trivial task, please be sure you really need these custom libraries.

Installing libxml2

NetPathMiner expects an environment variable LIB_XML or LIB_XML2 pointing to directory where libxml2 is installed. This directory should have both the compiled library (DLL file) and the header files.

You can download libxml2.dll from http://sourceforge.net/projects/gnuwin32/files/libxml/ among other sources. Please, place it in a bin folder under the installation directory.

You will need also the header files, which can be obtained from NPM_dependecies.tar file. After extracing it, copy the include directory to the installation directory.

Finally, set the LIB_XML2 variable to point to the installation directory, which should now contain dll files under bin and header files under include.

Installing libSBML

Since libSBML is a C++ libraries, it needs to be compiled using GCC compiler. Unforturantely, there is no binary version for Windows comipled with GCC. To use libSBML, you need to build it from source.

First, dowload source package from http://sourceforge.net/projects/sbml/files/libsbml/ , extract it. You will need also MinGW http://www.mingw.org/ or the 64-bit version http://mingw-w64.sourceforge.net/ depending on your system. Add mingw/bin to your PATH, by editing environment variables.

Second, you need CMake http://www.cmake.org/ . You can follow the instructions at http://sbml.org/Software/libSBML/docs/java-api/libsbml-installation.html#windows-configuring , however, choose "MinGW Makefiles" instead of "Visual Studio 10".

After finishing the CMake step, use the MinGW's make.exe to compile libSBML. Copy the dependencies you used during the compilation to the bin directory. Set the environment variable LIB_SBML to point the installation directory, which should now contain dll files under bin and header files under include

R Package dependencies

NetPathMiner depends on package igraph to represent network objects. Installing igraph is required for the package to work. You will also need devtools package to install directly from github. NetPathMiner suggests package rBiopaxParser to process BioPAX files and RCurl to download annotations from the web. NetPathMiner can still work without installing the suggested packages, but you will not be able to use the aforementioned functionalities.

igraph

Package igraph is available at CRAN. To install it call:

    install.packages("igraph")

devtools

Package devtools is available at CRAN. For Windows, this seems to depend on having Rtools for Windows installed. You can download and install this from: http://cran.r-project.org/bin/windows/Rtools/

To install R package devtools call:

    install.packages("devtools")

RCurl

For Unix users, make sure your Linux has library libcurl installed. Check out:

    locate libcurl   
    locate curl-config

If these are not found (usually the developer version is missing), most Linux users will be able to fix this by running:

    sudo apt-get install libcurl4-openssl-dev

You will now be able to install R package RCurl. In R console:

    install.packages("RCurl")

If you encounter other problems check out http://www.omegahat.org/RCurl/FAQ.html

rBiopaxParser

Package rBiopaxParser is available on Bioconductor. For installation instructions check out http://www.bioconductor.org/packages/release/bioc/html/rBiopaxParser.html or call:

    if (!requireNamespace("BiocManager", quietly=TRUE))
        install.packages("BiocManager")
    BiocManager::install("rBiopaxParser")  

to install it right away.

NetPathMiner Installation

If everything went well you will be able to install the NetPathMiner package.

From Bioconductor:

In R console, type:

    if (!requireNamespace("BiocManager", quietly=TRUE))
        install.packages("BiocManager")
    BiocManager::install("NetPathMiner")  

From GitHub using devtools:

In R console, type:

    library(devtools)   
    install_github(repo="NetPathMiner", username="ahmohamed")