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Hello Folks,
I realised this issue might be similar to https://github.com/hahnlab/CAFE5/issues/69#issuecomment-1487468573, but I think there are unsolved questions in the closed issues 69.
I found t…
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Hi,
I used --quantMode GeneCounts to generate a count table for my samples, after which I processed them with DESEQ2.
I noticed that a whole gene family is differentially expressed. (I think) T…
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Input: set of gene names, species tree?
Internally:
- fetch species absence/presence vector for each gene
- prune species tree or dim leaves with no genes
- schematically draw genes using different c…
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Mappings are available for both UniRef90 and UniRef50 gene families to the following systems:
MetaCyc Reactions
KEGG Orthogroups (KOs)
Pfam domains
Level-4 enzyme commission (EC) categories
E…
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non-redundant (NR) = 95% sequence identity
- if 1-to-1 mapping: we’re good
- if not: we need to do something more similar to Humann2
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Yes, this can be done via the gene search page, but if a user is focused on gene families, it may not be obvious to go use the gene search page instead.
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Hi!
I'm having some trouble understanding where this can come from.
I tried to align a sequence with HMMER and filter on the e-value at 1e-05.
With HMMER, I have this result in the domtblout:
```
…
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For the previous problem, I modified the mmseq.py file and changed it to：
if mmseqs_profiles_url is None:
mmseqs_profiles_url = 'file:///xxxx/PlasX_mmseqs_profiles.tar.gz'
if coefficients_url is…
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I ran PIRATE with 322 genomes (gff files) as input, but the file indicates 321 genomes. Is there any way to investigate why the count decreased from 322 to 321? The confirmation details are as follow…
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Now that I've found a workaround for #25, I have this error when I try to display a tree I have loaded in the db:
```
HTTP 404: Not Found [ http://localhost:3300/lis_gene_families/chado/msa/Test1-…