“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 firstname.lastname@example.org.
may also find the StickWRLD Manual
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
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.
FOR BEST RESULTS RIGHT-CLICK ON THE
DATA SET YOU WISH TO DOWNLOAD AND SELECT "SAVE"
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.