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Hello,
Thanks in advance for your help! I'm a newbie to this kind of work, so I apologize if I'm making a simple error. I am attempting to use orthologr for dnds calculation with the following inpu…
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I wish to show the phylogenetic relationship among some genes in HOGs using the corresponding gene tree in Resolved Gene Trees Directory, but I noted there are not bootstrap value on their nodes. Will…
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Hi,
First, I really like this package, thanks for putting it together!
I tried to use meta.retrieval but, if the list of genomes is quite long (e.g. all alphaproteobacteria) it never finishes be…
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Hi Bogdan, Michael,
I recently noticed this issue when TOGA annotates very short (varying lengths from 1bp on) transcripts.
For example rna-XM_025151385.1.5903 in vs_HLvidMac2/query_annotation.bed -…
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Hello - I would like to obtain a similarity metric between the pair of orthologue proteins detected by orthofinder or, even better, all the pairwise similarities in the input set of sequences. Is this…
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https://mp.weixin.qq.com/s/5rZ5yLXaLDVAtQbtGHAHoQ
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Hi, I want to have a python tree object of the ubergraph. What would be the recommended way to get there?
I have a solution, but it is very unsatisfying:
1. Using the ["https://ubergraph.apps.renc…
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To be discussed, following PMID:35622906
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Hi thanks for a great package! I understand that the functions `import_intercell_networks` and `nichenet_networks` return network knowledge for **human** that can be provided as input for cell-cell in…
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**Submitting author:** @wrightaprilm (April Wright)
**Repository:** https://github.com/wrightaprilm/treesiftr
**Version:** v1.0.0
**Editor:** @juanklopper
**Reviewer:** @ethanwhite, @rachelss
**Archiv…