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 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.
A minimum of 4GB physical memory is required for running FuSViz in user's machine (we recommend physical memory >= 8GB).
Run docker pull --platform=linux/amd64 senzhao/fusviz_shiny_app:1.8.0, 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 ..
Run docker run --platform=linux/amd64 --rm -p 4000:3838 senzhao/fusviz_shiny_app:1.8.0; 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.
NOTE: FuSViz docker image is built under amd64 platform, which may show a poor and slow performance 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.
A apptainer/singularity container of FuSViz is available for dowload, and we recommend run it using singularity version (>= 3.7.3):
singularity run fusviz_v1.8.0.sif 4000, then open web browser and input address.
NOTE: 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.
- R (>=4.0.0): https://www.r-project.org/; RStudio 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.
options(timeout=600)
if (! require('remotes')) install.packages('remotes')
remotes::install_github('senzhaocode/FuSViz')
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Install software library OpenSSL - a dependency of R package openssl
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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 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:
install.packages("openssl")
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Install software library libxml2 - a dependency of R package xml2
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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 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:
install.packages("xml2")
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Install software library libjpeg - a dependency of R package jpeg
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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 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:
install.packages("jpeg")
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Install software library libpng - a dependency of R package png
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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 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:
install.packages("png")
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Install software library libcurl - a dependency of R package RCurl
- Need for Debian or Ubuntu:
sudo apt install libcurl4-openssl-dev
- Need for Debian or Ubuntu:
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If users have a problem to install the dependency R package stringi (the latest release) for CentOS or RHEL automatically before FuSViz setup,
- Download the latest release stringi in *.tar.gz format locally, and run
R CMD INSTALL *.tar.gz
- Download the latest release stringi in *.tar.gz format locally, and run
source(file.path(system.file("app", package = "FuSViz"), "global.R"), local = TRUE, chdir = TRUE)
FuSViz_app()
A full description of FuSViz documentation is available:
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
t.cytotoxic AT gmail.com