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Hello author, thank you very much for your work. The code is very concise and elegant. I have a small question to ask you about projection matrices. Most of the camera reference matrices I come into c…
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## Reason
During mortar-based mechanical contact simulations, issue comes up sometimes with dual shape function calculation where the dual coefficient calculation may error out while inverting a …
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When running the `python setup_for_alphafold.py` script, the alignment performed by `tcrdock.sequtil.blosum_align` involves the deprecated `Bio.SubsMat` module, triggering the following warning at the…
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Add to the vignette "Using other data sources"
Potentially add a new class of data that helps define a contact survey.
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Hi,
would it be possible to output agent-level adjacency matrices (capturing contacts between agents) and SEIR status per time point?
This would be super useful to check advanced testing schemes t…
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Add ability to include known household age distributions as offsets in the 'home' setting model, in place of the whole population distribution (pop_age_to)
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Sometimes HiC data is stored in memory, in R in my case, as an actual matrix. It would be great if HiGlass supported matrix -> cooler conversion, preferably by allowing users to write their contact m…
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Dear authors, I am trying to reproduce the results in your publication and I was wondering if you can you please provide the structures and the corresponding code to reproduce the generation of the ma…
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We currently only do quasi time stepping, which simplifies a lot of things.
For actual time stepping we need further things like:
- time related matrices
- event management (contact)
- adaptivit…
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Hi,
Thank you very much for the development of this tool. I am facing an issue regarding the output format.
Here is the cmd line which I used:
HiCLift --input $file.cool --input-format coole…