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Hi There,
I am attempting to call cooltools.api.snipping.pileup(clr,features_df=peak_df , flank=300_000), where :
peak_df = pd.read_csv(f"ctcf.enhancer.promoters/{peak}.bed", sep="\t", names=['c…
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Use case:
* I'm building a simple gene expression network with DNAAssemblies, using OneStepGeneExpression for gene expression.
* I'm working with a Mixture instead of an ExpressionMixture, because…
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- EXP annotations to this term are here:
https://docs.google.com/spreadsheets/d/17UgKKsxtQveZW9o5cvqlaNpGS5Zx2ymZVkdW9vZjzxc/edit#gid=0
(Edited to make clearer):
GO:0006351 transcription, DNA-…
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Hi,
Thanks for Scenic+.
I am running the Scenic+ and getting an error on my data as well as the pbmc data after running
`from scenicplus.wrappers.run_pycistarget import run_pycistarget
run_p…
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I set status to partially_arrived, and you return it as all_arrived:
Printing description of dictParams:
{
"auth_token" = "j5rWiWcV7U3T3ASb_Knnwg";
guestlist = {
"actual_count_fem…
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Hi,
I wanna know if this tool can be used for drosophila samples? Like the -n parameter, can it identify genes from different species or the FlyBase gene ID?
Thanks!
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Dear Raymond,
I'd like to use `annotatr` for Arabidopsis thaliana, but I am not sure if this possible.
I have created a regulatory catalogue from an integrative analysis of Arabidopsis thaliana …
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I'll summarize our discussion below.
> CRO, Contributorship Research Ontology, an extension of CRediT, so perhaps it will gain traction, but probably at this point we should wait and see.
> they…
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Hello,
In running one of my samples through SCENIC+, I am running into an error in the run_pycistarget wrapper function, specifically at running DEM without promoters for topics_otsu where my value …
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http://www.leetchi.com/fr/cagnotte/creer