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Hi,
Nice pipeline! It is excellent to follow the methods/rules mentioned in the article to distinguish the types of binding (cobinding & tethered binding). So, do you have a ready-made script so we…
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Dear Authors,
It was mentioned in the paper that the
"Ultimately, our binding seed database was composed of approximately 250,000 helical motifs from which 140 million fingerprints were extracted…
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Hello!
I'm using modkit for a bacterial (epi)genomics project. I have a large, GC-rich bacterial genome with several methyltransferases which may or may not be expressed under culture conditions. …
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> @mtxellrb A script for creating a track database from bigWig TF ChIP-seq data is now added :`create_cistarget_track_databases.py`
>
> https://github.com/aertslab/create_cisTarget_da…
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hello,Michael
Thanks for your wonderful software.
In recent days, I want to use it for my analysis. I had installed it very well follow your instruction.
```
$REforge.py -h
usage: REforge.py [-…
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Following up on your previous question @biouserPD
To run sneep you need:
- the genome of your favourite organism in fast format
- a list of species specific TF binding motifs (PWMs) in TRANSFA…
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**Reported by kchris on 2010-06-12 00:00 UTC**
Hi,
There are some promoter motifs, e.g. the "A_box" that is part_of "RNApol_III_promoter_type_2" that are is_a children of "TF_binding_site", which is …
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Hi and thanks for developing this very useful tool!
when i tried to use snapatac2.tl.add_cor_scores(network, peak_mat= data) it gives me error of "'NoneType' object has no attribute 'obs_names'"
da…
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> ... transcription factor motif analysis was carried out with the FIMO package, with a p-value threshold of 0.001. A total of 614 human transcription factor binding motifs from the HOCOMOCO database …
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https://doi.org/10.1109/BIBM.2016.7822515 (https://arxiv.org/abs/1611.05777)
> Transcription factors (TFs) are macromolecules that bind to \textit{cis}-regulatory specific sub-regions of DNA promot…