[Bioc-devel] MotifDb missing some PWMs from FlyFactorSurvey database

[Shepherd, Lori]

Paul

  -  On the support site,  you can edit your profile and put package names as watchedtags.  When a person posts to the support site and tags with the package name you would then be emailed.   This assumes they tag the post correctly but also an option


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Paul Shannon <paul.thurmond.shannon using gmail.com>
Sent: Friday, June 5, 2020 1:12 PM
To: Nystrom, Spencer <snystrom using email.unc.edu>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] MotifDb missing some PWMs from FlyFactorSurvey database

Thanks, Spencer.  Sorry I missed the support posting - there�s no automatic forwarding from there to maintainers.

I�ll take a look at this later today, then post back to the support list, and we will get a fix in.

Thank you for pointing out the problem!

 - Paul

> On Jun 5, 2020, at 9:46 AM, Nystrom, Spencer <snystrom using email.unc.edu> wrote:
>
> Hi,
>
> I've identified a few missing PWMs from the MotifDb package and would like to help get them added. I posted on the support page but have not received a response after 10 days, so messaging here instead (link to forum post: https://secure-web.cisco.com/1TFAehHIfvF8C-fsHqKF9EZUlEaLQqYsIygNO_BAsoXZwv_Wu3u5B4wJVetP6b2oLhIIOFSZhhOumdKzED0ovgHBPNyPVtPXiHxRm8b66_DTxd3gOar2MNQ5l9qQH4_wqJMMJaxbnBCWUwAGnSDJO91ueABvVc6mU2FAghpGjUfBlWvlYMMhZzzmbgjYqsldl1Ta23cGowoJ3ncf7CeSKr6bKFMch5qHT0BqRq0t6Gi_b7w1KzlscAc0wC3Pxjq5gXX9vMchpSqTrtO3_MRw3Ojfo2wOimSuSsQL0RWe2mKIGnuSE0r8q7XSF0fsyFaH-DmeMbMdAxJok14mifZioaA/https%3A%2F%2Fsupport.bioconductor.org%2Fp%2F131312%2F). Full details can be found in the support post, but in summary, there are a small number of Drosophila transcription factors which do not have any entries in MotifDb, meaning anyone using that database for their motif analysis will not identify these factors as potential candidates. A .meme format file ("flyFactor_Missing_Motifdb.meme") of these missing motifs along with a reproducible script to identify these factors can be found at this gist: https://secure-web.cisco.com/1Hw4j-u2eWVf5hZXzqLZ4apPGgjUddOX5ixtNdTGwQZ4NPy_KaMZids5AaShi-S2meTRVKS9jM3cf2iEulIctx81-ZyEXDGgnDv79mSzGZG0QjWEwCoKwaCa8Eg2m1zL4AW14psIhbcmvxc36OZX77cPdvVBZBl0WIzqa0g6N2n6c75iPRS0Mi4k86awArVwZ6SMWbd9onXyqHQqqfNpEcQnilZw0UkOntlEVSBQWpNszEdDH6zw1gLuglq1F4JIJwa6onOYuveddTXIVT0r3veLCqhDXiDZIxFN9PmMrUUh9Xqiq2S2uRkK53JqfA-krBLQfCwo4agchyGpfqwWZOA/https%3A%2F%2Fgist.github.com%2Fsnystrom%2Fb7701858bec6bc4ce7758a7582422359. I am happy to help curate any additional metadata required to get these factors added to the database.
>
> Best,
>  -Spencer
>
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>
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