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Most of the functionality exposed by the Motif Finder project needs to be executed in different steps. In fact, one of the steps requires the user to execute the graph mining algorithm of choice.
By…
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Cross reference #898.
File ``Bio/motifs/thresholds.py`` was originally checked in as ``Bio/Motif/Thresholds.py`` by Bartek Wilczynski (@barwil) and was credited copyright 2008 by Norbert Dojer:
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I see a lot of cases when a TF has motifs falling into distinct clusters. Is there a preferred strategy to select the likely correct WT motif for each TF and allocate each TF to one motif cluster?
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vitkl updated
2 years ago
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1. change status 'COMPLETED' to 'ARCHIVE';
2. remove old analysis while keeping the results.
dshao updated
9 months ago
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Hello, Thank you for developing a great tool.
I have run DRUMMER with my data and obtained several output folders. I used the same command line for DRUMMERS for both sample 1 and sample 2.
However…
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### Discussed in https://github.com/GreenleafLab/ArchR/discussions/1319
Originally posted by **wuv21** March 3, 2022
Hi!
Been running into an issue similar to #562 and #483 with the same e…
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https://doi.org/10.1101/172767 (http://www.biorxiv.org/content/early/2017/08/06/172767)
> Determining the binding locations of regulatory factors, such as transcription factors and histone modifica…
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## Hierarchy of RE
```
LTR (Family) —> L1 (Sub-Family) —> L1_Rod (Gene) —> L1_Rod_dup1 (Transcript)
LTR (Family) —> L1 (Sub-Family) —> L1_Rod (Gene) —> L1_Rod_dup2 (Transcript)
LTR (Family) —> L1 …
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That would be great for people to get a better understanding of their graph topology and to reason which algorithms make sense to run on it.
- apoc.degree.stats for all the relationships and direct…
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### [Transcription factors](https://www.youtube.com/watch?v=Sd3imcsvXxI)
1. Transcription factor (proteins) control the expression of genes by regulating the process of gene transcription.
![gene-…