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Regulons can be thought of as a set of multiple hypotheses - the action of TF A modulates B,C,D ... Z genes.
Finding a source with a compatible reuse license will be key
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pySCENIC processes that need to have a seed parameter added:
- [x] grn (https://github.com/aertslab/pySCENIC/commit/920a6a54f322d095af658f02ce3d1674ae85e9c2)
- [x] ctx
- [x] aucell
These requi…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/TransBioInfoLab/MethReg
Confirm the following by …
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I want to use pySCENIC for bulk RNAseq tumour samples.
I am thinking that the major issue will be optimizing the threshold for the enrichment score and then the regulon activity score.
I will …
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When I run
```
!pyscenic ctx adj.csv \
{f_db_names} \
--annotations_fname {f_motif_path} \
--expression_mtx_fname {f_loom_path_unfilt} \
--output Step6_reg.csv \
--mask_dro…
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SCENIC:MULTI_RUNS_TO_LOOM__TRACK:AUCELL crashes when no signatures passed the filter.
```
Error executing process > 'single_sample_scenic:SCENIC_append:SCENIC:MULTI_RUNS_TO_LOOM__TRACK:AUCELL (1)'…
ghuls updated
4 years ago
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Hi Bram,
I have a similar request, in my case the Regulons are the most important output from this pipeline, and I need to have them in a human readable format. I've looked for the JSON export comm…
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Hi,
The current version of the Consensus TF regulons data (`CTFRs_v122016.rdata`) is not compatible with the package of functions from `lib_enrichment_scores.r`. `CTFRs_v122016.rdata` is a list of …
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Dear developers,
Is there a way to make a regulon object based on my specific set of TF and their targets?
Thank you!