FuSViz

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A web-browser app to visualise, interpret and prioritise genomic/transcriptomic structural variations (SVs) of multiple samples.

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![FuSviz_overview](https://raw.githubusercontent.com/senzhaocode/FuSViz/master/logo_white_back.png)

### Overview

A shiny app to visualise, interpret and prioritise genomic/transcriptomic structural variations (SVs) of multiple samples. It provides multiple solutions and an interactive user interface to **1)** review SV quality via read alignment of a single sample, and **2)** investigate the prevalence and recurrence of SVs and their relevant genes in a cohort of cases. The tool is designed for combining SVs called from DNA-seq (e.g. whole genome or target exome) and RNA-seq to illustrate a biological implication of SVs to the host genes and interested genomic regions in context of various annotations, and it can also integrate a mutation profile (SNVs/Indels) to reveal a connection between small variants and complex genomic aberrations.

### Getting a quick start

#### <ins>Prerequisite for FuSViz running</ins>

A minimum of **4GB** physical memory is required for running *FuSViz* in user's machine (we recommend physical memory **>= 8GB**).

#### <ins>Deploy with docker/podman</ins>

##### Pull pre-built FuSViz image (release version) from docker hub

Run `docker pull --platform=linux/amd64 senzhao/fusviz_shiny_app:2.0.0`, then check the image by typing `docker images`

Optional: if user would like to build *FuSViz* image (developmental version), just download soruce code and change to directory `cd ~/FuSViz-master`; then run `docker build --platform=linux/amd64 --rm -t senzhao/fusviz_shiny_app:latest -f Dockerfile .`.

##### Launch FuSViz app

Run `docker run --platform=linux/amd64 --rm -p 4000:3838 senzhao/fusviz_shiny_app:2.0.0`; then open web browser and input address `127.0.0.1:4000`. If TCP port 4000 on 127.0.0.1 of the host is occupied, users can use other port values to bind port 3838 of the container.

<ins>NOTE:</ins> *FuSViz* docker image is built under amd64 platform, which may show [a poor and slow performance](https://stackoverflow.com/questions/70765522/docker-amd64-warning-on-apple-m1-computer) in Apple M1/M2 machine (arm64 platform). Before pulling and running the image, we recommend enable the feature of **Use Rosetta for x86/amd64 emulation on Apple Silicon** for Docker Desktop - Navigate to **Settings** in Docker Desktop and check **Use Rosetta for x86/amd64 emulation on Apple Silicon** in the **General** tab.

#### <ins>Deploy with apptainer/singularity for Linux distribution</ins>

A apptainer/singularity container of *FuSViz* is available for [dowload](https://fusviz.s3.eu-north-1.amazonaws.com/fusviz_v2.0.0.sif), and we recommend run it using singularity version (>= 3.7.3):

`singularity run fusviz_v2.0.0.sif 4000`, then open web browser and input address.

<ins>NOTE:</ins> the *FuSViz* apptainer/singularity container is specific for running under **Linux OS (e.g. Debian, Ubuntu, Redhat and CentOS)**, which is incompatible with **Apple M1/M2 machine**. Users have to use the **Docker/Podman** container to run *FuSViz* under Mac OS.

#### <ins>Deploy without container</ins>

##### Requirement

* R (>=4.0.0): https://www.r-project.org/; [RStudio](https://rstudio.com/products/rstudio/download/#download) is recommended but not mandatory. 
* For windows users, if an earlier version of R (< 4.0) is present in the system, please uninstall it firstly and make sure only R >=4.0 is available.

##### Installation

options(timeout=600)
    if (! require('remotes')) install.packages('remotes')
    remotes::install_github('senzhaocode/FuSViz')

##### IMPORTANT NOTE for Linux OS, some libraries need to be installed properly before setup FuSViz.

1. Install software library [OpenSSL](https://www.openssl.org) - a dependency of R package [openssl](https://cran.r-project.org/web/packages/openssl/index.html)

* For **Debian or Ubuntu**: `sudo apt-get install -y libssl-dev`; For **Fedora, CentOS or RHEL**: `sudo yum install openssl-devel`
    * If root privillege is not available, users have to download [source code](https://github.com/openssl/openssl) and install at $HOME directory. For example,
    
            ./Configure --prefix=/OpenSSL_path --openssldir=/OpenSSL_path/ssl
            make && make install
            C_INCLUDE_PATH=/OpenSSL_path/include
            export C_INCLUDE_PATH
            LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/OpenSSL_path/lib
            export LD_LIBRARY_PATH
            LIBRARY_PATH=$LIBRARY_PATH:/OpenSSL_path/lib
            export LIBRARY_PATH
            
    * Install R package [openssl](https://cran.r-project.org/web/packages/openssl/index.html): `install.packages("openssl")`

2. Install software library [libxml2](http://xmlsoft.org) - a dependency of R package [xml2](https://cran.r-project.org/web/packages/XML/index.html)

* For **Debian or Ubuntu**: `sudo apt-get install libxml2-dev`; For **Fedora, CentOS or RHEL**: `sudo yum install libxml2-devel`
    * If root privillege is not available, users have to download [source code](http://xmlsoft.org/downloads.html) and install at $HOME directory. For example,
    
            ./configure --prefix=/libxml2_path # if ./configure file does not exist, please run ./autogen.sh --prefix=/libxml2_path instead.
            make && make install
            C_INCLUDE_PATH=/libxml2_path/include
            export C_INCLUDE_PATH
            CPLUS_INCLUDE_PATH=/libxml2_path/include
            export CPLUS_INCLUDE_PATH
            LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/libxml2_path/lib
            export LD_LIBRARY_PATH
            LIBRARY_PATH=$LIBRARY_PATH:/libxml2_path/lib
            export LIBRARY_PATH
    
    * Install R package [xml2](https://cran.r-project.org/web/packages/XML/index.html): `install.packages("xml2")`

3. Install software library [libjpeg](https://ijg.org) - a dependency of R package [jpeg](https://cran.r-project.org/web/packages/jpeg/index.html)

* For **Debian or Ubuntu**: `sudo apt-get install libjpeg-dev`; For **Fedora, CentOS or RHEL**: `sudo yum install libjpeg-turbo-devel`
    * If root privillege is not available, users have to download [source code](https://ijg.org) and install at $HOME directory. For example,
    
            ./Configure --prefix=/libjpeg_path --libdir=/libjpeg_path/lib --includedir=/libjpeg_path/include
            make && make install
            C_INCLUDE_PATH=/libjpeg_path/include
            export C_INCLUDE_PATH
            LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/libjpeg_path/lib
            export LD_LIBRARY_PATH
            LIBRARY_PATH=$LIBRARY_PATH:/libjpeg_path/lib
            export LIBRARY_PATH
            
     * Install R package [jpeg](https://cran.r-project.org/web/packages/jpeg/index.html): `install.packages("jpeg")`

4. Install software library [libpng](https://libpng.sourceforge.io) - a dependency of R package [png](https://cran.r-project.org/web/packages/png/index.html)

* For **Debian or Ubuntu**: `sudo apt-get install libpng-dev`; For **Fedora, CentOS or RHEL**: `sudo yum install libpng-devel`
    * If root privillege is not available, users have to download [source code](https://libpng.sourceforge.io) and install at $HOME directory. For example,

./Configure --prefix=/libpng_path
            make && make install
            C_INCLUDE_PATH=/libpng_path/include
            export C_INCLUDE_PATH
            LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/libpng_path/lib
            export LD_LIBRARY_PATH
            LIBRARY_PATH=$LIBRARY_PATH:/libpng_path/lib
            export LIBRARY_PATH
            
     * Install R package [png](https://cran.r-project.org/web/packages/png/index.html): `install.packages("png")`
 
5. Install software library [libcurl](https://curl.se/libcurl/) - a dependency of R package [RCurl](https://cran.r-project.org/web/packages/RCurl/index.html)

* Need for **Debian or Ubuntu**: `sudo apt install libcurl4-openssl-dev`

6. If users have a problem to install the dependency R package [**stringi**](https://github.com/gagolews/stringi) (the latest release) for **CentOS or RHEL** automatically before *FuSViz* setup,

* Download [the latest release](https://github.com/gagolews/stringi/releases) **stringi** in \*.tar.gz format locally, and run `R CMD INSTALL *.tar.gz`

##### Launch FuSViz App

source(file.path(system.file("app", package = "FuSViz"), "global.R"), local = TRUE, chdir = TRUE)
    FuSViz_app()

#### <ins>Usage & manual</ins>

A full description of *FuSViz* documentation is available: &nbsp;&nbsp; [![Documentation Status](https://readthedocs.org/projects/fusviz-docs/badge/?version=master)](https://fusviz-docs.readthedocs.io/en/master/)

#### <ins>Online tutorial videos</ins>

[![IMAGE ALT TEXT HERE](https://raw.githubusercontent.com/senzhaocode/FuSViz/master/Tutorial_video_link.png)](https://www.youtube.com/watch?v=GAZInLru4y4&list=PLSOEIThRcIXUnPedL9VZWxuOJy3vU9y6a)

### Citation

Sen Zhao, Sigve Nakken, Daniel Vodak, Eivind Hovig, **FuSViz—visualization and interpretation of structural variation using cancer genomics and transcriptomics data**, *Nucleic Acids Research*, Volume 53, Issue 4, 28 February 2025, gkaf078, https://doi.org/10.1093/nar/gkaf078

### Contact

t.cytotoxic AT gmail.com

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