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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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* 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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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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Dear Francisco
I'm working on a project where I wish to use MAGs to create a community GEM (6 species). The MAGs will be obtained from somewhere else, and I want to use that data to create the mod…
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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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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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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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**Supervisor:** Bérénice Batut
**For degree:** Bachelor
**Status:** Open
**Keywords:** Metagenomics, microbiome, data analysis, training
# Global context
Emerging and powerful technologies li…
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Fantastic opportunity and we're very keen to contribute! I'll set up a folder for the Australian Microbiome Initiative and provide links to all of our current ASV workflows (16S, 18S, fungal ITS), alo…