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Hey @olivertam oliver~
I have some questions here that I would like to ask you. It is mainly about the interference of TE on gene expression. I think the modes in which TE may interfere with gen…
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Hi, I'm having trouble downloading Hi-C data for chromosome 9 specifically using juicebox. When I use juicebox, it creates 2 files (chr9.KRobserved.gz. and chr9.KRNorm.gz) respectively, but both files…
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- Github URL: https://github.com/lucyzhang95/BioThings_TTD_Dataplugin
- Git Branch/Commit: master fab9df6
- No. Documents: 889851
- Structure of documents: 3 records
```python
{
"_id": "D07OAC…
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[PLACE MANUSCRIPT AND EDITOR DETAILS HERE WHEN AVAILABLE] See step 3
[PLACE PDF URL HERE WHEN AVAILABLE] See step 7
## Step 1. Inform bioRxiv
Who can help: @QueenKraken, @nlisgo, @scottaubrey
- [x…
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**Describe the bug**
I am trying to run scenicplus on a Pig dataset. I have generated motif scores following the steps in `create_cisTarget_databases` `. I had to make multiple changes in the codeb…
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Hello, thank you for designing this powerful algorithm. I managed to run the entire pipeline using the example files without a problem, but when I run it on my files I am receiving this key error belo…
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Hi there,
Many thanks for creating the tool - excellent work! I have a few questions about using it with my data.
I have ATAC-seq and H3K27ac ChIP-seq from three individuals (biological replicat…
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I am running `vembrane table` on a VCF file and get the following error message:
```
Traceback (most recent call last):
File "/usr/local/lib/python3.10/site-packages/vembrane/representations.py…
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Hi,
Various matrices are used in snapatac2's tutorial:
Features: creating a cell by bin matrix containing insertion counts across genome-wide 500-bp bins.
gene activity: generates cell by gene ac…
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Users may want to analyze the set of cis pairs, i.e. the set gene-gRNA pairs in close physical proximity. This is especially likely to be the case in enhancer-targeting screens.
To this end, we shoul…