Recent Posts

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31
General Discussion / Multicollinearity
« Last post by amathelier on September 07, 2018, 07:13:59 am »
Hello,

I would like to use the Transfactivity tool from the REDUCE suite. One concern that I have is that if you use a large set of matrices (PWMs), some will be very similar and so can induce multicollinearity in their scores at promoter regions, and it will introduce multicollinearity between them in the multiple linear regression analysis. If so, then the activities of each TF associated to the similar PWMs might be wrong. Any insight/advice on how to tackle that? It does not seem that you take that into consideration in the previous usage of the tool.

Thanks
Best
AM
32
General Discussion / Re: download previous versions of REDUCE_Suite
« Last post by xiangjun on August 16, 2018, 08:44:17 pm »
Hi Kate,

Sorry, no previous versions of the REDUCE_Suite are available for download.

May I know what you want to achieve with the original Convert2PSAM -source=v1 option, possibly with a concrete example?

Xiang-Jun
33
General Discussion / download previous versions of REDUCE_Suite
« Last post by knie on August 16, 2018, 11:58:56 am »
Hi Xiang-Jun,

I'm wondering if there's a way to download the old versions of REDUCE_Suite. I need the `Convert2PSAM -source=v1`option, which was removed in the latest update.

Best,
Kate
34
General Discussion / Re: availability of FeatureREDUCE?
« Last post by hjb2004 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
35
General Discussion / Re: availability of FeatureREDUCE?
« Last post by pk 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.
36
Documentation / Re: Other utility programs
« Last post by xiangjun on July 18, 2018, 07:53:14 am »
Hi,

Type ProcessFASTA -h for more info. Check the source code for technical details.

Best regards,

Xiang-Jun
37
Documentation / Re: Other utility programs
« Last post by Millson on July 18, 2018, 07:45:10 am »
Hi Xiangjun, do you have more resources to share on ProcessFASTA? Cheers.
38
General Discussion / Re: availability of FeatureREDUCE?
« Last post by xiangjun 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
39
General Discussion / availability of FeatureREDUCE?
« Last post 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!
40
General Discussion / Re: Error when generating logos in PDF format
« Last post by xiangjun on February 11, 2018, 09:53:30 am »
Quote
I can't directly read LogoGenerator-created EPS file on Linux. Am I missing something?

Could you be more specific? Please provide a concrete example so I (and others) can reproduce what you failed to achieve.

Best regards,

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