Omics Data Analyser
This is an R program to visualize and analyze omics data such as those from microarray, metabolomics and proteomics experiments. Next-generation sequencing such as RNA-Seq experiments are to be supported in the future. The input of this program is intensity or count data supplied in a list or table along with parameter settings, all in an Excel file. The output is an Excel file with figures and analysis result sheets.
Current version: 1.7.3. Tested R version: 4.0.2
How to run this tool:
Step 1: Download all files from this website and save them all in a folder.
Step 2: Make a copy of the data template file and open it in Excel. Read the instructions in there. Make sure Excel Macros are allowed.
Step 3: Copy your data to the RawData sheet of the template. Data can be a list or table with samples, features, feature descriptions and values. See data template for details.
Step 4: Fill out the Parameters, Comparisons, Features, and Samples sheets as necessary.
Step 5: Run the program with your data and save results in an Excel file. If visualization is enabled, a Figures folder will be created to save the plot files in the postscript format (.ps). See below for ways of running the program.
- Running on the BioHPC @ UTSW. Log on the BioHPC Portal, launch a Web Visualization node, open a terminal from there, and run the following:
sh /path_to_the_program/run_analysis.sh /input_path/input_data.xlsm /output_path/results.xlsx optional_BioHPC_queue_name
- Running on your local machine. Make sure R is installed and you can run R script from a command line tool such as a Linux terminal or Windows CMD / PowerShell:
Rscript /path_to_the_program/ODA_version.R /input_path/input_data.xlsm /output_path/results.xlsx
Examples: See the Examples folder for example input and output files.
Contact Zhiyu Zhao for comments / questions / suggestions.