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Updating microbiome data analyses
As our databases and knowledge of biodiversity (taxonomy and function) grow, it is imperative to reassess
previously analyzed data that relies on these databases. Thi…
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Mon Sep 30 15:48:59 UTC 2024, there were errors when running autoupdate
Cannot autoupdate workflows/computational-chemistry/gromacs-dctmd, last line of stderr is
bioblend.ConnectionError: Unexpected…
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Connect NMDC EDGE to core NMDC orchestration services
NMDC EDGE61 is currently powered by a cluster computing service managed by SDSC. We will implement
automation functions in NMDC EDGE to execute wo…
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Hi microbiome team,
Over in dada2 land we are interested in linking our package with other excellent Bioconductor microbiome packages. The primary way we have done this so far is to integrate "stubs"…
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Supporting microbiome-specific data containers in R; in particular [_phyloseq_](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0061217) (more widely used) and [_TreeSummarizedExperi…
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We support a Contribution Annotation Framework that allows us to indicate roles of conributors. However, many tutorials still use the "old" style contribution metadata (without roles)
Updating this…
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There are some issues with this training that I collect here to fix step-by-step.
* In the preprocessing part, all fastq outputs go into multiQC, but since multiQC only shows one output for identical…
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* humann nucleotide and protein database: https://github.com/galaxyproject/usegalaxy-tools/issues/855 (missing on AU/ORG)
* kraken2 - 5 toturials, multiple DBs - should all be updated to 2024 version…
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Hello,
I was hoping you might have some advice about understanding an issue I am running into with some microbiome samples (fungal community in soybean at ITS region).
The issue has to do with i…
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Enhanced, improved and novel NMDC workflows to advance microbiome science
Similar to the entire field of genomics, all NMDC workflows (Appendix 15) are subject to an iterative
improvement process. To …