REDUCE Suite
General Category => General Discussion => Topic started by: pk on July 17, 2018, 05:34:01 pm
-
If possible, I'd like to try running FeatureREDUCE (https://doi.org/10.7554/eLife.06397).
The Riley lab points to the older Bussemaker lab "Software" page (http://rileylab.org/featurereduce/), but that appears to be defunct. I assumed I'd be able to download the software from this forum along with the remaining REDUCE software suite. It doesn't appear to be in the downloadable tar balls. Should I not be trying to use FeatureREDUCE to analyze PBM data, i.e. is it excluded from the REDUCE suite for a reason, or am I just not seeing it?
I found a GitHub repo for the project (https://github.com/FeatureREDUCE/FeatureREDUCE), but it appears to be untouched since 2015 (the paper is still listed as "in revision" in the README). Is the GitHub repo the newest/only available implementation?
Thanks for the help!
-
Thanks for posting your FeatureREDUCE question(s) on the REDUCE Suite Forum. Unfortunately (and as you noticed), FeatureREDUCE is not available from the basic REDUCE Suite which includes MatrixREDUCE/MotifREDUCE and some accessory programs. I was not involved in the development of FeatureREDUCE and its support (if any) is not covered by the Forum (I've made this point clear from the announcement page (http://reducesuite.bussemakerlab.org/announcements/reduce-suite-v2-2-is-available/)). Sorry for not being able to provide you with a more positive answer.
Xiang-Jun
-
Thanks, Xiang-Jun, for the response!
I'll try asking the first author of the FeatureREDUCE manuscript about the current status of the software/project.
-
Hello PK,
The latest/only version of FeatureREDUCE is indeed still the 2015 version on GitHub:
https://github.com/FeatureREDUCE/FeatureREDUCE
You may also be interested in No Read Left Behind (NRLB), the latest algorithm from our lab:
https://github.com/BussemakerLab/NRLB
https://www.ncbi.nlm.nih.gov/pubmed/29610332
Best regards,
Harmen Bussemaker