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Hi, I am trying to run TOBIAS to analysis my time-series ATAC-seq data, it ran well with ATACorrect and FootprintScores, but reported some errors in BINDetect step. In short A. it could not write the…
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Before we start updating DRAO, we need to update the member ontologies and ensure there are no resulting conflicts. This ticket covers that update.
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https://mp.weixin.qq.com/s/zt-5JshP71ZX3OwPOsfagA
ixxmu updated
3 years ago
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In GO we have
GO:0017091 | AU-rich element binding
and
ARE binding | exact
An ARE binding motif has a very defined consensus (conserved from yeast to human), so maybe we should add that…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/ibn-salem/chromloop
Confirm the following by edit…
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mating type M-box ACAAT
This is a very common motif, so it is hitting *everything*
The real region must be much longer I presume? If we could extend the motif to something more sensible we would e…
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Hello!
I have a set of TFBS that I have already been using for other analyses that were identified using a different TFBS search tool than is used in BINDetect, but I was hoping to use BINDetect to…
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I'm wondering if there's a workaround when dealing with a low # of peaks. The tool works great normally, but if I evaluate a specific subset of ATAC peaks (~600 in total) that are relevant to the ques…
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**Is your feature request related to a problem? Please describe.**
At the end of the pipeline it is always a great idea to visualise the results. Gigabytes of text data are OK for us to work with but…
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Hi, developers:
Thanks for developing this excellent package for ATAC-seq footprinting. This package is powerful and seamless across different steps. However, recently I found the `ATACorrect` not …