Stefano Ghignone

Thanks for the explanation Zachary! In the case of only two comparisons, I can identify my differentially abundant taxa as follows, i.e. padj > 0.05 and Log2FoldChange > 2.5 (upregulated)...

Hi Zachary, sorry for extremely slow reply, > I saw you posted this to the google groups and in that question you asked about filtering out NAs as well. You...

```r per_taxon_max_change 0.05)) { return(0) } else { return(max(abs(per_taxon_fold_changes[[i]][per_taxon_p_values[[i]] This would preserve only taxa that have a change (positive or negative) of greater than 2.5 associated with a p value...

Thanks Zachary for the follow-op. Both functions run without warnings or errors, but I get them downstream. 1) first function version ``` > per_taxon_max_change 0.05, na.rm = TRUE)) { +...

I also verified that GetBibEntryWithDOI does not retrieve **_keywords_** nor **_abstract_**, even when they are present in bib files downloaded from publisher website. Is it possible to have those fields...

dear developer, I have the same request: is it possible to have the map for the taxonomy of the 5s and 5.8s rfam ? Thanks a lot in advance

Are there also separate taxonomy files for the new databases or I have to extract it from the fasta files? I'm finding some missing taxonomies, e.g. in the file smr_v4.3_sensitive_db_rfam_seeds.fasta....

hi guy, I'm interested in this topic too. Any news?

Thanks Christoph, I just realized the stupid reason for which my command wasn't successful. Anyway, I have a couple of questions. Why if I use nad6 as seed the program...

I'm also interested in this option. Moreover, I'm interested in using not only PE libraries, but also MATE pair libraries with different insert sizes. Any news?