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The locate_unlinked() function is a bottleneck for various analyses. It should be possible to write a multi-threaded implementation using dask.
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Hi John, I written some report_sim() examples below that demonstrate the 'subscript out of bounds' error that I encounter. It is very possible that I'm misusing the function, but there potentially cou…
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# Challenge 34 - Regional to Urban Air Quality Mapper
> **Stream 3 - Software Development for Earth Sciences applications**
### Goal
Develop an application capable of improving (downscaling) th…
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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4874657/pdf/nihms755930.pdf
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Hi,
When I ran scAbsolute with the default ploidy window I noticed that a lot of cells (~50%) had copy number of 1 across the genome, which is not something we expect to see in the samples (blood c…
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Hi,
Using latest version of nlmixr2, I simulate data and then try to estimate the posthoc random effect values for the simulated dataset. I was using the same parameter values for simulation and p…
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Currently the advice for what to do when certain iterations of a scenario don't converge (defined by either big gradients or non-positive definite Hessian) is to simply drop them and run more. I think…
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Hi!
I'd like to calculate nucleotide diversity for different population. I install ANGSD by follow the following the instructions:
git clone https://github.com/samtools/htslib.git
git clone htt…
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See Adrien's paper:
https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0099-4
as described in the paper, the term “sensitivity” is polysemic. It may be good to keep the term as a par…
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Hi,
I have noticed that at loci with non-sparse situations both `susie_stuff_stat` and `susie_rss` takes forever to converge to the default ELBO tolerance of `tol=0.001`, relaxing this to `tol=0.0…