Haris Zafeiropoulos
Haris Zafeiropoulos
To build a wf that could be partially used, I am trying to have some conditions and provide alternative input files for the case a user has already or hasn't...
## Expected Behavior A working-fine workflow to perform smoothly with the `--provenance ` argument. ## Actual Behavior When the `--provenance` argument is used, the workflow breaks. ## Workflow Code This...
Check [repo](https://github.com/jfmrod/mapseq) and [publication](https://doi.org/10.1093/bioinformatics/btx517)
This is about describing the PEMA outputs in a formal way, so that they are more machine-interoperable. Similarly to the `parameters.tsv` file and its structured format (see issue #35 )...
This issue is about describing the parameter file that is required to run PEMA in a machine-interoperable way: describing the formats and including defaults for all entries in the file,...
Consider of adding as an alternative the Midori dbs the [Eukaryote CO1 Reference Set For The RDP Classifier](https://github.com/terrimporter/CO1Classifier).
Hi there, I am trying to figure out the Pareto optimality script of yours. I was wondering if there is any chance that in [line 74](https://github.com/opencobra/cobratoolbox/blob/master/src/analysis/multiSpecies/microbiomeModelingToolbox/pairwiseInteractionModeling/computeParetoOptimality.m#L74) `rxn2` should be replaced...
Hi DRAM community. I just noticed that there is a bug in [DRAM 1.5.0 release](https://github.com/WrightonLabCSU/DRAM/releases/tag/v1.5.0) on the DRUM-setup.py script. Here is the issue: https://github.com/WrightonLabCSU/DRAM/blob/7735a04e58c300d53f9d3611a583b48e507bb843/scripts/DRAM-setup.py#L123C6-L126C66 as you can see there are...
It has been observed that the current setup (we'll call it `original` approach), can be time consuming. In cases of hundreds of samples this can be a limiting factor for...
Consider a normalization of 16S results using https://rrndb.umms.med.umich.edu