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Excellent work on this! The ability to plot data.frame objects is incredibly efficient for feature selection and making edits as desired. Just a few major improvement requests:
1. When multiple fea…
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not an issue but a general inquiry. Can one use `clusterBidirectionally` to map bidirectional promoters? bidirectional promoters are classically defined as 1kb regions between 2 opposite TSSs(+ and - …
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As noted by @mhvk [here](https://github.com/numpy/numpy/pull/26102#discussion_r1534636116), the order that promoters get added matters, and it shouldn't.
Taking a look at the promoter resolution al…
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Related to #30
need GTF file
can we keep info about each promoter? remove ones with no reads. rather than just summarize across all promoters. could then extract genes with high promoter activi…
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1- Most should be describable as nucleotide mutations (not urgent)
2- Some can be moved to "promoter swap" if we create a type for that? but should we consider the purpose of the swap (i.e to over…
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### Prerequisites
+ [ ] Have you read [Feedback](https://guangchuangyu.github.io/chipseeker/#feedback) and follow the [guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/)?
* [ ] ma…
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It has been a while since I have noticed that a few entries would not be returned despite being present in the genome file.
E.g. I would not get promoters back when querying "chrXHg123456" if the loc…
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Allow promoters to select locations pre existing within the system
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Thanks for making and maintaining pharokka and phold!
* pharokka version: 1.7.1
* phold version: 0.1.4
* Python version: 3.10.14
* Operating System: Red Hat Enterprise Linux 8.8 (Ootpa)
### D…
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Hi again,
While investigating the `proActiv` results for my sample dataset I came across the fact that many genes do not have a "Major" promoter, yet they tend to have multiple Minor promoters.
…