gapseq
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jotech
Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
Hello, ## Technical part While working on the reconstruction of metabolic networks from public genomes of the NCBI database, I have found that gapseq (`version 1.2` with subcommand `doall`) uses...
Hi @jotech! I just wanted to ask how dat/media/gut.csv was formulated? Is it based on metabolomics results from fecal samples?
Hi, I have successfully run gapseq, but was wondering if there is a way to output an annotated genbank file with the identified genes used in the model? Or even...
The threshold for when pathways are considered complete seems to be hardcoded into the R scripts. Would it be possible to make this an input parameter so that it can...
Hi, I am still having some problems with gapseq adapt. I generated a draft model and when I use gapseq adapt this is the output I get: `Warning in add_growth(mod.out,...
Before my questions, I would like to thank to all developers of this wonderful tool :) I'm trying to check whether there is positive/negative correlation in growth between Species A...
Hi, Not an issue but a few questions on the seawater recipe and adding other related media. How was the existing "meerwasser" recipe made, or what was the reference? https://github.com/jotech/gapseq/commit/5d0aeafc3d40a0430aaed84b4f6eb9aba2549df6#diff-d82c35c23e1d05980fc5b6b31e9b25b406f669fdf8c34a76805931fc784ae6a4...
