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Having a user interface during the course was pretty convenient. I was wondering if NG-Tax can still be accessed through Galaxy, and if so, on what web address? I searched through all of the course material and did a fair shair of Googling, but I haven't been able to find the Galaxy-version of NG-Tax anymore. Does it still exist?
(I could only find https://galaxy.wur.nl/galaxy_production/ but that does not include NG-Tax in its tools.)

We need to test a dataset used with the current latest version of NG-Tax.
Wasin might be able to provide with such a set?

under 07-MAW-PV1.Rmd, Interference for microbial network using SpiecEasi, i having some issue with the modularity in network (starting on line 264).

net.c
Pulsar-selected refit of sparseiCov
Path length: 20
Graph dim: 679
Criterion:
stars... sparsity 0.016

mod.net <- net.c$refit

when i trying to run this line at 272,

colnames(mod.net) <- rownames(mod.net) <- colnames(otu.c)#you can remove this
it prompt me an error message, Error in rownames<-(*tmp*, value = c("OTU-9410491526:Bacteroides", : attempt to set 'rownames' on an object with no dimensions

I check on the mod.net, realised 2 of my Dimnames are in NULL type, as shown below

mod.net[["stars"]]@Dimnames[[1]]
NULL
mod.net[["stars"]]@Dimnames[[2]]
NULL

if i skip the rowname, proceed until line 276, No matter the add.rownmanes is TRUE or FALSE also the same error message.

stool.ig.mod <- graph.adjacency(mod.net, mode='undirected', add.rownames = TRUE)
Error in mde(x) : (list) object cannot be coerced to type 'double'

May i know how to fix this? Thank you

Hello

Thanks very much for sharing this course workflow for analysing microbiome studies.
Is there any possibility to let me know how to work with SPIEC-EASI code used for network analysis after deprecating some parts of the function?
net.c <- spiec.easi(otu.c, method='mb', icov.select.params=list(rep.num=50))

Many Thanks
Marwa

dear Sir,

i've encounter the following error code

Error in combn(seq_along(lev), 2, simplify = FALSE, FUN = function(i) lev[i]) :
n < m

when i run the following code:

L.pairs <- combn(seq_along(lev), 2, simplify = FALSE, FUN = function(i) lev[i])

it was all ok until this step.

would you kindly help?

thank you.

The section 1.2 Useful functions/resources has link to List of R tools for microbiome analysis. A typo in the repository name for List of R tools for microbiome analysis website. Now the link is broken in book. correct link is here

i'm about to get ready with the course but i encounter this error:
Error: Failed to install 'microbiomeutilities' from GitHub:
(converted from warning) cannot remove prior installation of package ‘Rcpp’
would you kindly help?