There are many files changed in this PR since this PR is re-running all the notebooks using the latest version of the Pseudomonas dataset after our collaborators have finalized QC filtering. We have updated our notebooks to use this latest version to be consistent and reproducible.
No heavy review needed, all these notebooks have been reviewed previously. The results look similar to previously and these can be seen in the figures figure_generation/output/. The one notable difference is there is a decrease in signal strength looking at core genes related to accessory genes. After a little digging into the differences between the datasets used it looks like its a difference in the samples included, but a manual spot check into these experiments did not show any obvious reasons.
There are many files changed in this PR since this PR is re-running all the notebooks using the latest version of the Pseudomonas dataset after our collaborators have finalized QC filtering. We have updated our notebooks to use this latest version to be consistent and reproducible.
No heavy review needed, all these notebooks have been reviewed previously. The results look similar to previously and these can be seen in the figures
figure_generation/output/. The one notable difference is there is a decrease in signal strength looking at core genes related to accessory genes. After a little digging into the differences between the datasets used it looks like its a difference in the samples included, but a manual spot check into these experiments did not show any obvious reasons.