GeneLab_Data_Processing
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nasa
**Draft currently until i get confirmation this fixed it from the individual who hit the issue.** - fix to single-end humann3 run where the ref db for metaphlan needs to...
Some datasets can have over 1,000 files in the MAGs and bins folders of the Assembly-based_processing directories (for example: https://genelab-tools.arc.nasa.gov/jira/browse/GLDATAPROC-694). There's no need to have all of them available individually.
- an issue can arise if the user is pointing to previously installed humann3 reference databases, or if the locations were manually changed for testing at some point - this...
Hi, I'm running this pipeline from the SJSU HPC and I'm having an issue where ~8.5k out of my 29k rows of data are populating with both the symbol and...
## Description This file has been retired as the relevant columns are now generated on the fly where used by GeneLab visualization. ## Proposed Solution Remove generating code.
## Description Current default output directory is named after GLDS ID; however, with release of OSDR, the default directory should indicate both the OSDR and GLDS IDs by default. ##...
## Description Factor value strings can collapse into the same R safe strings. E.g. "p53+/Fbxw7+/-" and "p53-/Fbxw7-/-" Both collapse into "p53..Fbxw7..." This breaks DESeq2 R scripts. ## Steps to Reproduce...
## Description Certain datasets have experimental groups of single samples. This current breaks differential expression approaches and likely means differential expression will be impossible. ## Steps to Reproduce 1. Create...
Transfer from dev issue 149 - [ ] Annotation Reference Table Support