« previous next »
Pages: [1]

Author Topic: availability of FeatureREDUCE?  (Read 118083 times)

pk

  • with posts
  • *
  • Posts: 2
    • View Profile
availability of FeatureREDUCE?
« 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!
Logged

xiangjun

  • Administrator
  • with posts
  • *****
  • Posts: 42
    • View Profile
Re: availability of FeatureREDUCE?
« Reply #1 on: July 17, 2018, 06:58:47 pm »
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). Sorry for not being able to provide you with a more positive answer.

Xiang-Jun
« Last Edit: July 17, 2018, 07:07:31 pm by xiangjun »
Logged

pk

  • with posts
  • *
  • Posts: 2
    • View Profile
Re: availability of FeatureREDUCE?
« Reply #2 on: July 18, 2018, 03:11:44 pm »
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.
Logged

hjb2004

  • Administrator
  • with posts
  • *****
  • Posts: 5
    • View Profile
Re: availability of FeatureREDUCE?
« Reply #3 on: July 18, 2018, 04:34:12 pm »
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
Logged
Pages: [1]
« previous next »
 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊]. See also http://forum.x3dna.org and http://x3dna.org