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For the "Enhancer-gene predictions" table on the Variant and Gene pages:
Remove "model == ENCODE_EpiRaction" from the displayed results table
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The links after the subheading "Enhancer-Gene Prediction Target Genes: " do not lead to valid gene pages
e.g. https://catalog.igvf.org/rs1250566?sub=4674b28efb10e477977543d82a87a45b37ed2eff49f66861ba…
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Hi
I downloaded the K562 Hi-C result: [ENCFF621AIY.hic](https://www.encodeproject.org/files/ENCFF621AIY/) from ENCODE.
Then I ran **juicebox_dump.py** for compute the **hic_gamma** and **hic_scal…
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Dear developer (Rongxin),
I am impressed by the package that it can compute the peak-to-gene link. You mentioned in the tutorial that '# convert the pair to genome browser arc plot format'. What is…
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Hello @kaizhang and thank you for this great software. I am curious if you have any vignettes available that walk through some of the downstream functions like
`tl.link_tf_to_gene` or `tl.add_tf_b…
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- Could we create a "Predicted Enhancers" section to replace the "Regulatory Regions" section? Then we can show elements that are predicted to regulate the gene (as on the variant page), rather than …
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Hey!
Thank you for this great package!
I ran my multiomic data with the stream pipeline and found that it got stuck when generating igraphs.
Specifically in the part below. Any idea?. (I used >…
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Thanks for a great easy to use tool. I've finally reached the step where I would like to do a Gene Centric Noncoding conditional analysis on some select rare variants I identified in my data set.
As…
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proposed definition:
A transcriptional cis regulatory region (ranges from 0.5kb to 3kbp) that when located between an enhancer and a promoter, the insulator prevents the enhancer from modulating expre…
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I got an error when using —— setGenome("hg19") :
Configure bsgenome ...
Configure bsgenome finished
Configure motifpwm ...
Configure motifpwm finished
Configure motifPWMOBJ ...
Configure motifPW…