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Hi
I don't think GO:0030509 BMP signaling pathway should have the parent term GO:0006357 regulation of transcription from RNA polymerase II promoter when the definition for BPM signaling states that…
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Hello developers,
I was wondering if one wants to use Seekr to analyse the kinetics of binding/unbinding/rebinding to a target receptor; is it possible?
Say I have 10-20 mdcrd files of my protein-…
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OpenMM fails to build the System for some unconventional amino acids.
```
pdb = PDBFile(sys.argv[1])
ff = ForceField('amber99sb.xml', 'tip3p.xml')
system = ff.createSystem(pdb.topology)
Traceback (m…
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_The following is draft until this text is deleted._
Meeting Nov 27th 2020 at 2pm UK time at https://ucl.zoom.us/j/92800004715. This page follows on from #41 .
Recording is [here](https://youtu…
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Could I please ask if OmnipathR provides access to a list of gene pairs?
That is, I would like to get a dataframe where each row corresponds to a pair of genes (or proteins), e.g., *CXCL10* and *CX…
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Hi Harold
Can you fix this please? metalloendopeptidase activity (GO:0004222) has 22 EC xrefs (and 21 Metacyc xrefs and 93 Reactome xrefs). Should just be EC:3.4.24.
id: GO:0004222
name: meta…
sjm41 updated
3 years ago
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Potentially very useful. Not sure why we don't have it yet... Maybe too many? Probably make sense to activate once we have a proper UI for the filters.
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I have single cell data from rhesus macaque that I want to analyze using nichenet. Currently, I am using organism="human". Of the roughly 19,000 genes I have in my Seurat object, roughly 13,000 of the…
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Dear authors,
Thanks for this wonderful package!
I'm confused about the receptors of ligand-to-target signaling paths. There are some receptors existed in the inferred ligand-to-target signaling pat…
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Meeting Nov 20th 2020 at 2pm UK time at https://ucl.zoom.us/j/92800004715. This page follows on from #40 .
Recording is [here](https://youtu.be/oz5Ikf_bxdw).
On the call: @mattodd @danaklug @ed…