“StickWRLD as an interactive visual pre-filter for canceromics-centric eQTL data” 

Rumpf, R. W., Wolock, S., and Ray, W. C.  2014.  Cancer Informatics (pending).

In order to view the dataset below, please be sure that you have already downloaded StickWRLD from the StickWRLD home page.  You will have to have python installed on your computer in order to run StickWRLD.  If you would prefer to have access to a downloadable VirtualBox Virtual Machine (an Ubuntu instance pre-configured to run StickWRLD) please email the author at wolfgang.rumpf@nationwidechildrens.org.

You may also find the StickWRLD Manual of use.

Once you have both StickWRLD and the datasets downloaded, you can use the "load" command to load the data.  As per the StickWRLD Manual:

1.  Launch StickWRLD (e.g. from the command line type python stickwrld_demo.py while in the StickWRLD directory)
2.  From the Data Loader pane, select "Load..."
3.  Load the data set itself by selecting the file RWR-CI-Data.aln (with no separator selected) or RWR-CI-Data.csv (with the comma separator selected)
4.  Once that's loaded StickWRLD wants you to load the headers file which contains the column descriptors for the display - select RWR-CI-headers.txt
5.  The StickWRLD GUI should now load.  NOTE:  it may take 30 seconds or so on a Core2Duo system, less on a more modern computer.

If you encounter any errors please be sure you have correctly installed StickWRLD as per the manual.


Below are two different formats of the data - both contain the same information, but one (the aln) is not comma separated, where the other (the csv) is.  The csv version is included so that you can open the file in a spreadsheet application for browsing, if desired.



As described in the paper, this dataset has been encoded into a format which could be read by StickWRLD.  The StickWRLD manual describes the process of encoding any dataset into the StickWRLD format.  If you are planning on loading biological sequence information (e.g. protein or DNA alignments created in Clustal), you may convert your Clustal alignment file to StickWRLD format using this fasta2stick.sh shell script (requires Mac OS X or linux).

The StickWRLD Data Format/Loading your own Data

For more information on creating custom datasets for use in StickWRLD please see the StickWRLD Manual.