Comments (5)
cmkobel
commented on September 3, 2024
For at gøre det, er jeg nødt til at finde en måde at udføre functional enrichment som ikke er artsspecifik.
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cmkobel
commented on September 3, 2024
Nu har jeg prøvet at stille et spørgsmål om arts-uspecifik-sammenligning i slack microbioinfo.
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cmkobel
commented on September 3, 2024
Dette kan være en del af min kommende HGT pipeline. Hvis et plasmid har en bestemt funktionalitet, kan man argumentere for at miljøet har selekteret det ind i organismen.
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cmkobel
commented on September 3, 2024
Functional enrichment er stoppet med at virke på grund af r-dependencies. Må fixes.
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cmkobel
commented on September 3, 2024
New solution using the full KEGG hierarchy and diamond-uniref-ko mapping is deployed and works well.
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Related Issues (20)
- Upgrade to snakemake 8 HOT 1
- Can't add more than a single string (file or glob) to the input_genomes parameter. HOT 2
- rule gtdb_download: curl: (77) error setting certificate file: /etc/ssl/certs/ca-bundle.crt HOT 1
- mamba requirement is unnecessarily specific HOT 1
- Prune test datasets
- Remove busco?
- N<4, iqtree: ERROR: It makes no sense to perform bootstrap with less than 4 sequences. HOT 1
- gtdbtk: mash: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory HOT 1
- wget should not use --continue, but somehow otherwise never write to an alternatively named file.
- Naming of output directory. HOT 4
- Roary policy HOT 1
- Implement downloading ko00001.json HOT 2
- Option to add .faa files for analysis downstream of gene calling
- hat?
- Migrate to codeberg HOT 2
- Remove mamba as dependency from bioconda recipe? HOT 1
- Follow the standard file hierarchy for a snakemake pipeline. HOT 3
- Benchmarking
- Returns exit code 0 on error. HOT 2
- --help HOT 2
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