Samuel Degregori
Samuel Degregori
Awesome. Thank you for the pointers @agitter @dhimmel . Somehow I never noticed the other repositories and am now using manubot quite easily. The git part I am still learning...
Hi all, I am having a similar issue. I can also make a separate post if necessary. Basically I am trying to install Rcall and getting the error: ``` julia>...
Please forget I exist.....
Wait maybe I am not that crazy. So now when I run this analysis I've been trying to run I get the same error about RCall not being properly compiled....
I would compare the relative abundance values which hopefully should be the same before and after...Ive seen wonky things like this too in phyloseq where abundances will double or cut...
not sure but there have been multiple posts showing that unifrac in phyloseq is unreliable see [here](https://forum.qiime2.org/t/very-different-weighted-unifrac-results-for-qiime2-versus-phyloseq/4591). So I would use vegan in R to generate the unifrac plot. I...
are you able to use qiime2 at all? I have this issue all the time with large datasets and qiime2 actually has built in functions to prune your table to...
nope but I am now using the DESeq2 pacakge in R on its own and it has been working fine for me
Prune samples will literally just filter out samples with less than 500 reads while rarefying will normalize all your samples to have exactly 500 reads. In my experience I use...
I think you can treat your factor as an actual R factor. this explains how to reorder factor levels where in this case, phyloseq@sam_data$sampleid would be your factor and your...