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I want to somehow see the phenotypes of the the homologs and how they compare to the gene page that I am on. Not sure if this is a new instance of phenogrid or how to display this, but its clear we ne…
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## Background
Currently in NGB, user can explore (work with) genes in different ways - e.g. via viewing at the "Browser" or in the "Genes" panel.
It would be convenient not just view info about th…
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I was trying to find a way to retrieve the orthologs for a single input gene (no constraint on the target organisms).
Input gene: RGD:3889
Input taxon: 10116
Started loading, then timeout. Appa…
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For the MVP, we want to simplify things as much we can, and having organisms from multiple taxonomies can be very complicated, because of gene orthologs, different conventions in naming and coordinate…
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The log-likelihoods for identical trees vary. This leads to rejection of one tree, while another is kept (I only checked the AU-test). A different extreme - identical trees have very similar likelihoo…
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Hi Dr. Guan,
I'm running your software on a large genome with ~20% duplicated orthologs as ID'd by BUSCO. The input data are PacBio CLR reads. I am seeing minimal improvements on duplicates, can yo…
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Hi! I hope all is going good!
I am trying to run gimme motif2factors (v0.17.1, installed through conda/mamba) on the genome of my organism to be able to run ANANSE. I set up a folder for a custom …
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Hello all -- I've been doing some test runs using non-KO orthologs, and while they seem to be working as expected, I have not been able to locate the snakemake logs. Could you clarify where they're wr…
padbc updated
3 years ago
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i think it would be really great if the homolog tab could indicate if there is phenotype data for any of the genes listed. at first, a simple icon to indicate that there's phenotype data available wo…
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As a user I would like to be able to call a serach API enpoint and be returned all results _and_ all orthologs of those results. The endpoint should have the same query parameter specification as `/se…