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### 08/09/2021, Anshul, Jay, Tao, Shannon, Annika
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I think we've discussed this in the past, but I didn't see an issue commemorating it. The basic idea is that there are things like repeats (or other features that may be of interest in some specialize…
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Hi, I am currently working on Cut&RUN data (with custom reference) with two different histone antibodies and trying to apply them to TFcomb. Here is some start codes as documentation. I used H3K4me3 a…
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Hi,
I am trying to use msCentipede on a ATAC-seq time course series without success. I get an error when running a command like
python call_binding.py --task learn --protocol ATAC_seq testbk/Ctcf_…
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- [ ] What types of knowledge and/or algorithms do we want to compute?
- [ ] specificity prediction algorithms
- [ ] gather comprehensive list of existing tools
- [ ] which algorithms will require cod…
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# Li, Dong, Wu et al. 2016
## bioRxiv
*http://doi.org/10.1101/086421*
## Abstract
> Characterizing the binding behaviors of RNA-binding proteins (RBPs) is important for understanding
thei…
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Hi,
Maybe I'm getting this totally wrong, but from the README file it seems that to annotate regulatory regions for each gene or region, you can either use a motif annotation generated by cluster-b…
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We need to pull a series of data to inform which genes to look for variants in.
There is a[ google doc here](https://docs.google.com/spreadsheets/d/1yX-5sfrC3vrahf4_k7-5rl4Oqzm853ollIMmUo1PTc0/edit…
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Exact same problem as described here: https://www.biostars.org/p/9577755/
The whole AUC matrix are 0s
```
pyscenic grn --num_workers 25 expr_mat_1.tsv allTFs_hg38.txt --transpose -o expr_mat…
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After running FeGenie with a reference database (nr.dmnd) I get the error shown below.
As an output I get the complete FeGenie-summary.csv and an empty file FeGenie-summary-altered.csv.
I think I…