GEView

(Intuitive microarray and NGS gene expression data viewing tool for biologists)

Created by: Libi Hertzberg, Assif Yitzhaky (Domany group, Weizmann Institute of Science) and Metsada Pasmanik-Chor (Head of Bioinformatics Unit, Faculty of Life Science, TAU).

Platforms: Windows, Linux.

General Description:

GEView is a simple tool for visualization of expression data. It serves all available platforms, given that expression values for each gene/microRNA/protein are provided in a tab-delimited file as input, after pre-processing and normalization. The purpose of this tool is to enable the Bio-Med researchers with no computer-science skills, to intuitively visualize high-throughput data produced in their wet experiments, in a convenient and simple manner. It performs basic quality control steps such as Principal Component Analysis to evaluate the experiment results and batch effect correction.  On top of all, it uses ANOVA to identify genes which are differentially expressed between the various experimental conditions. It provides immediate visualization of all genes' differential expression in the various experimental conditions together with ANOVA p-values, through a click on the gene in the output Excel file. In order to complete data visualization, links are also provided for GeneCards, UCSC and NCBI genome browser databases, for each specific gene.

 

 

Installation instructions:

Windows (64 bit):

1.     Download and install MCR (Matlab Component Runtime for Matlab R2018a) from here.  (NOTE: If you already have this MATLAB version installed of your computer, step 1 can be skipped).

2.     Download GEView_windows_v5b_021218.zip   

         Extract to some folder. Enter “GEView” folder and launch (click) run.bat (may take a moment).

3.  Optional step - do this only if you intend to use batch correction: download and install R for Windows (64 bit) from: http://cran.r-project.org/bin/windows/base/

 

Linux:

1.   Download and extract GEView_linux_v5b_021218.zip to some folder.

 Enter to the folder GEView and verify that those files are executable:

chmod +x geview_app

chmod +x  run_ geview_app.sh

 

2.      If MATLAB R2016a is NOT installed on your computer:

A. Download and install MCRInstaller.zip (Matlab Component Runtime), by typing:

unzip MCRInstaller.zip

 ./install

B.  From the folder GEView execute the following at the command prompt:

./run_geview_app.sh <mcr_directory>

<mcr_directory> is the directory where MCR is installed. For example, if MCR is installed in /MATLAB_Runtime/v901

Run the shell script as:

 ./run_geview_app.sh /MATLAB_Runtime/v901

 

         If MATLAB R2016a is installed on your computer:

From the folder GEView execute the following at the command prompt:

./run_geview_app.sh <matlabroot>

<matlabroot> is the directory where R2016a is installed on the machine (you can use the Matlab command “matlabroot” in order to find out.

For example, if your MATLAB is installed in /MATLAB/R2016a

Run the shell script as:

./run_geview_app.sh /MATLAB/R2016a

 

                3.  Optional step - do this only if you intend to use batch correction:

A. Download and install R for Linux from: https://cran.r-project.org/

B. Install the “sva” package by entering R and typing (try http:// if https:// URLs are not supported):

source("https://bioconductor.org/biocLite.R")

biocLite("sva")

 

Link to Help page

Example files: (in order to download a file, right-click on the file link and choose “save as…”)

                Input Example: Zurich_HD_TEL_E2A_data_labeled.txt

                Output Example: results_Zurich_HD_TEL_E2A_data_labeled.xlsx

                Input Example for Batch Correction: StJude_Zurich_example_batch.txt

 

                Source code (MATLAB m-files): GEView_code_v5b_021218_mfiles.zip

                Launch by typing “geview_app” from MATLAB.

                Note: if you intend to use batch correction or the help menu, please extract the source files into the folder “geview_app” which is generated after extracting the standalone package (Windows or Linux, see above).

 

For support please contact Assif Yitzhaky: