Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/sritchie73/NetRep

R package containing functions for assessing the replication/preservation of network topology for weighted gene coexpression network modules in one or more independent datasets through permutation testing.
https://github.com/sritchie73/NetRep

Last synced: 8 days ago
JSON representation

R package containing functions for assessing the replication/preservation of network topology for weighted gene coexpression network modules in one or more independent datasets through permutation testing.

Awesome Lists containing this project

README 

        
# NetRep

##### Fast permutation procedure for testing network module replication



An R package containing functions for assessing the replication and 

preservation of a network module's topology across datasets through 

permutation testing. This is suitable for networks that can be meaningfully 

inferred from multiple datasets. These include gene coexpression networks,

protein-protein interaction networks, and microbial interaction

networks. Modules within these networks consist of groups of nodes

that are particularly interesting: for example a group of tightly

connected genes associated with a disease, groups of genes

annotated with the same term in the Gene Ontology database, or

groups of interacting microbial species, i.e. communities.

Application of this method can answer questions such as; (1) do

the relationships between genes in a module replicate in an

independent cohort? (2) are these gene coexpression modules

preserved across tissues or tissue specific? (3) are these modules

conserved across species? (4) are microbial communities preseved

across multiple spatial locations?



The main function for this package is `modulePreservation`, which 

performs the permutation test procedure. Other useful functions include 

`networkProperties` for calculating the topological properties of a 

module, and `plotModule` for visualising a network module.



For more information see the associated publication in Cell Systems,

[A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets](http://dx.doi.org/10.1016/j.cels.2016.06.012). 



## Installation



The latest stable version of NetRep can be installed either directly from

CRAN or from this GitHub repository:



```{r}

# From CRAN

install.packages("NetRep")



# Alternatively From GitHub

library(remotes)

install_github("InouyeLab/NetRep")

```



Developmental / pre-release versions of NetRep can be installed from this repository:



```{r}

library(remotes)

install_github("InouyeLab/NetRep", ref="devel")

```



Older versions of NetRep can be installed by specifying the version number in the `ref` argument:



```{r}

install_github("InouyeLab/NetRep", ref="v0.61.0")

```



## Package Tutorial



A vignette (tutorial) is available online at [vignettes/NetRep.md](vignettes/NetRep.md),

or can be loaded directly from R by running `vignette("NetRep")` if you have installed

the package from CRAN. 



If you are installing NetRep from GitHub and wish to make the vignette available on your 

local machine, you will need to install `rmarkdown` and specify `build_vignettes=TRUE` 

when running `install_github`.



## Installation troubleshooting



**NetRep** and its dependencies require several third party libraries to be

installed. If not found, installation of the package will fail.



 1. A compiler with `C++11` support for the `` libary.

 2. A `fortran` compiler.

 3. `BLAS` and `LAPACK` libraries.

 

### OSX



The necessary `C++11` compilers are provided with the `Xcode` 

application and subsequent installation of `Command line tools`. The most

recent version of OSX should prompt you to install these tools when 

installing the `devtools` package from RStudio. Those with older versions of 

OSX should be able to install these tools by typing the following command into 

their Terminal application: `xcode-select --install`.



The necessary `fortran` compiler depends on both the OSX version and R version

installed by the user. The ["R for Mac OS X" page on CRAN](https://cran.r-project.org/bin/macosx/tools/)

provides instructions for determining the correct fortran version as well as 

relevant download links. 



### Windows



**NetRep** can be installed on Windows in R version 3.3.0 or later. The 

necessary `fortran` and `C++11` compilers are provided with the `Rtools` 

program. We recommend installation of `NetRep` through `RStudio`, which should

prompt the user and install these tools when running 

`remotes::install_github("InouyeLab/NetRep")`. You may need to run this 

command again after Rtools finishes installing.



### Linux



If installation fails when compiling **NetRep** at `permutations.cpp` with an 

error about `namespace thread`, you will need to install a newer version of 

your compiler that supports this `C++11` feature. We have found that this works

on versions of `gcc` as old as `gcc-4.6.3`.



If installation fails prior to this it is likely that you will need to install

the necessary compilers and libraries, then reinstall R. For `C++` and 

`fortran` compilers we recommend installing `g++` and `gfortran` from the

appropriate package manager for your operating system (e.g. `apt-get` for 

Ubuntu). `BLAS` and `LAPACK` libraries can be installed by installing 

`libblas-dev` and `liblapack-dev`. Note that these libraries **must** be

installed prior to installation of R.