Antônio Camargo

Given that Prokka has a `--metagenome` option, I'd expect that partial gene sequences would be predicted. Maybe Prodigal's `-c` argument could not used when executing prokka with the `--metagenome` argument....

@sjmgarnier Thanks for the reply. I understand your point concerning the diverging colormaps, I didn't know that this was a design choice. What do you think of the inclusion of...

@sjmgarnier Having the same level of gray in both ends is precisely the point of this colormap. As a circular colormap, twilight starts and ends on the same color (this...

I'm getting this error in the latest devel. `Error in solve.default(t(X) %*% X) : Lapack routine dgesv: system is exactly singular: U[4,4] = 0`

It worked. Thanks Warren! Is there a reason that the new p-value aggregation prevents `sleuth_to_matrix` from returning gene-level abundance values? I understand that this method doesn't use gene-level expression for...

Hi @lynnyi I understand that the p-value aggregation strategy doesn't use gene-level abundances for the statistical analysis, but I think users may be confused that they're doing gene-level analysis and...

@mschilli87 I agree with you that gene-level TPM values do not make sense in this kind of analysis, but I'm not certain that making it impossible for the user to...

I can confirm that the alphabetical order determines the signal of the beta values. These are the results of the same test that I performed twice, just changing the name...

You can get that using the [`sleuth_to_matrix`](https://www.rdocumentation.org/packages/sleuth/versions/0.29.0/topics/sleuth_to_matrix) function: `tpm_matrix

Sorry for the late follow-up. The values that in get with `sleuth::get_bootstrap_summary` match the ones in the figure and are different from the ones I get with `sleuth_to_matrix`