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I am watching [this talk](https://www.youtube.com/watch?v=dNnHlb4RfJY) from EuroPython 2023. I believe that use cases shown there could be adapted to SquidPy. For example, make interactive scatter plo…
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This cluster was found in #7 as strong (+/-) correlation in both ORF and CRISPR but not (completely) strongly connected in the KG.
Looking across ORF and CRISPR plots there, there are a few other …
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Annotations to 'transcription' and 'regulation of transcription' should normally be mutually exclusive.
Here are gene products annotated to both 'transcription' and 'regulation of transcription'…
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From #7 we see that ZBTB16 & SLC39A1 are strongly anti-correlated in ORF data and CRISPR data, and it's novel (not seen in Evotec KG).
Zinc finger and BTB domain-containing protein 16
SLC: Zinc t…
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# Scenario 6: Regnets for gene expression and regulation
A fundamental theory in molecular biology, known as the ‘the central dogma’, describes gene expression as the flow of information from DNA t…
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**UniProt UniRule (ID and label):**
GO:0032968 | positive regulation of transcription elongation from RNA polymerase II promoter | IEA with UR00063877
**Sequences with problematic annotation (ID…
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When clusterProfiler was enriched, the genes in the R package did not have this GO annotation. After enrichment, this gene appeared in the GO entry in the result. I want to know how the corresponding …
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* **PTHR ID & PTN node:**
GO:0003712 | transcription coregulator activity | IEA with PTHR10782:SF97 | GO_REF:0000118
GO:0006357 | regulation of transcription by RNA polymerase II | IEA with PT…
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Hi Jean,
I just have one (I guess) simple question that I do not manage to understand.
In the results file from scde.expression.difference, I can not see if up- and down-regulated genes come from …