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Hi,
Thank you for developing this tool. I tried to run Scenic+ on my mutiome data and I got an error message that I don't quite understand.
Could you help me with this issue.
Thanks in advance
Thi…
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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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```
biocbuild@kunpeng1 ~/git> R CMD build --keep-empty-dirs --no-resave-data ELMER
* checking for file ‘ELMER/DESCRIPTION’ ... OK
* preparing ‘ELMER’:
* checking DESCRIPTION meta-information ... O…
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RSAT `position-analysis` detects k-mers that present any type of positional heterogeneity by running, for each k-mer, a chi-squared homogeneity test on its profile of counts per positional windows com…
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Imagine a tool reports some new TFBS motif. You want to know what molecular programs are controlled by the TF in question. Extract regions that follow the most common DNA motif and perform gene ontolo…
mlist updated
5 years ago
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Currently, we can perform motif enrichment analysis for 200bp flanking regions of the differentially spliced exons. Let us create an option so that we can specify the length of the target regions as w…
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1. How consensus footprint is derived? Why do we want target factor peaks to overlap with consensus footprint?
* do we consider consensus footprint as background?
* TF peak regions > footprint >= mo…
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Hi, I am running the Scenic+plus pipeline with Zebra fish and I am getting `Unable to load annotation for custom` warnings when I run `run_pycistarget`
All databases created specifically for Zebra …
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I have a few TFs that appear to be missing from the TF list seen in this file: hs_hgnc_tfs.txt, which is available in the resources folder. The TFs are:
ZFHX4
AEBP1
CXXC5
TSHZ2
They are also mi…
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**Use case**
I have a series of ChIP-seq samples that I eventually want to perform differential peak calling and motif enrichment analysis upon between different treatment groups (and input).
*…