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Dear Dr. Derelle,
Thank you for your work with Broccoli.
Quick question, is there support for a user-supplied blast directory, like `orthofinder -b`? I'd like to port my orthology pipelines to Bro…
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This thread to serve as a request for a presentation at the next Data Stewards / DCPPC call on Alliance for Genome Resources (AGR) Supplement Aims. Specific Aim 3: "Develop the AGR Disease Navigator t…
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As I see it now, the only thing that has to be updated is then the orthology management between networks in the same species. Right now complex (the command line tool) does not calculate conservation …
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Hi,
I would like to report a problem I encountered recently with one of my workflows when using individual conda environments for different rules which should be installed inside a globally defin…
reslp updated
11 months ago
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It appears that orthologous relationships are only added to nodes present in the network at the start of Phase III. geneAbundances added to the network via "gene scaffolding" are not getting connected…
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Hi all,
I'm using phyloseq to analyze some metagenomic data for potential microbiome function analyses. I have a phyloseq object that has the KEGG orthology ID and per sample counts of annotated gene…
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We use HGNC Comparison of Orthology Predictions (HCOP) tool to get the mouse gene -to- human gene mappings.
Currently, we use `HGNCHCOP` as the SAB for the relationship between the mouse and human …
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Yeast has
RNA polymerase I core factor complex (GO:0070860)
A RNA polymerase I-specific transcription factor complex that is required for the transcription of rDNA by RNA polymerase I. In yeast the …
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I thought I'd come up with a great solution to allowing Ortholog Phenotypes, showing a checkbox to include ortholog phenotypes as well.
Unfortunately, there's no way to get to the checkbox if th…