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Hi!
I used the following command to run the VarGen pipeline but I am getting the following error:
```
> disease_variants disease_annotation
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https://github.com/wtsi-hgi/Automated-Enhancer-Gene-SCRAMBLEr/blob/69f34beb08b5967cffc060e5e753a46c276f8cf0/region_convolutions.py#L56
This line is too convoluted, it should be broken down into sep…
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Hello, I have used some of the new features of plotPeakProf2.
It could be able to compare the peak distribution in self-made Grange objects such as the enhancers region.
But if it could accept t…
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Hello, I have data generated from RNA-seq, ATAC-seq and H3K27ac ChIP-seq assays for the same mouse tissue and would like to try EAGLE to link putative enhancers to target genes. In the Usage you ment…
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Hi,
Before it worked fine, but this time, it shows error:
```bash
localrule region_to_gene:
input: /lustre1/project/stg_00079/students/tingting/data/sun/snap2_allfragments/08/080results_s…
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Supporting a GFF file like this:
```
1 araport11 mRNA 52061 54689 . + . ID=transcript:AT1G01110.1
1 araport11 exon 52061 52730 . + . Parent=transcript:AT1G01110.1;Name=AT1G01110.1.exon1;constitutiv…
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Xiaotao,
I am using neoloop to produce some neo-loops and neo-tads (some rows with the last columns as "1"). But I am interested in validate whether they are really neo-loops/ neo-tads that are r…
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Hi,
I am interested in your developed tool "PSYCHIC". However, I am confused about this output files. According to your description, I checked ".enh_p.bed" file. It seems the output is as followed:
…
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**Describe the bug**
A clear and concise description of what the bug is.
**To Reproduce**
```python
if 'region_to_gene' not in scplus_obj.uns.keys():
log.info('Inferring region to gene re…
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> **Background.** Gene expression is mediated by specialized cis-regulatory modules (CRMs), the most prominent of which are called enhancers. Early experiments indicated that enhancers located far fro…