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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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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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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…
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Hi, I have some issues with interpreting the output files of prediction: there are EnhancerPredictionsAllPutative.tsv, EnhancerPredictionsFull_threshold0.02_self_promoter.tsv, and EnhancerPredictions…
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Hi
Thank you for your wonderful paper.
When I check you Zenodo directory (https://zenodo.org/records/7351632), I find three columns ("effect" and "p-adj" and "Significant") in the file `Fulco_i…
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It will be great if it can show a custom track, like the UCSC genome browser.
Updated:
My goal is to check whether SV break an enhancer or not. Currently, it is not easy to get the location of a …
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Hi @kkdey,
I have following questions on GSSG pipeline. It is great if I can hear when you have a chance.
1. Regarding the generation of gene program .txt file from .csv. https://github.com/kkde…
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> To visualize multiple regions (e.g., a Topic, or an enhancer signature): the
> total accessibility can be viewed in the tSNE, similarly as a gene signature
> in SCope v1. For, the genomic view of …