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Hi, I'm trying to use PROseq data which is basically experession data instead of using ChIPseq data, but the problem I'm running into is I don't understand what kind of Normalization you used in ChIPs…
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Hi, I'm encountering an issue while creating visualizations in Gosling.js using BED files processed through HiGlass. Specifically, the positions of the annotations in the visualization appear to be in…
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Paper: https://www.nature.com/articles/s41592-023-01938-4
Abstract:
Joint profiling of chromatin accessibility and gene expression in individual cells provides an opportunity to decipher enhancer-d…
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**Describe the bug**
"Hi, I am trying to use region_to_gene in the Snakemake pipeline, but I encountered an error: 'ValueError: Input y contains NaN.'"
**To Reproduce**
```bash
scenicplus grn_…
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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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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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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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I got an error when using —— setGenome("hg19") ：
Configure bsgenome ...
Configure bsgenome finished
Configure motifpwm ...
Configure motifpwm finished
Configure motifPWMOBJ ...
Configure motifPW…