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Stefan in my lab is using texmexseq. For [this otu table](https://gist.github.com/elsherbini/c1a1228c6036064b55ed90fea63d003e) the F transform fails for one of the samples, but if we use the `f.transf…
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Hi,
I'm using SourceTracker in R for the first time and can't work out an error I'm getting when using the sourcetracker() function on my own data (works for example data though):
Error in if (s…
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Given the challenge of formatting all of the data exactly as required for `mbImpute()`:
* condition
* vector in the same order as the sample order used for the OTU table
* OTU
* "wide" matr…
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```
With single quotes:
$ bpipe run batch_merge_replicates.groovy ./otus/ggsilva/otu_table_ggsilva.qiime
org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
script_f…
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The output from dada2 leaves me with an OTU, taxonomy and sample information file. I'm trying to create a phyloseq object from these 3 files using:
OTU = otu_table(spc, taxa_are_rows = TRUE)
TAX…
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Dear yijuanhu,
I would like to use the LDM package to analyze data processed by other normalization methods (e.g. CSS), do I need to add the following parameters in the `ldm()` function, such as:
`…
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Congratulations on the publication and thank you for sharing your code and data!
I tried tab 'sTable8', 'sTable10' from the supplementary table in place of files "20190307_CR_NICU/201903_NICU_combi…
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I have a request for some code. Basically, I want some way to highlight intrapersonal variation through time. I know the within versus between unifrac distances says that variability within an individ…
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Good day,
I read your recent paper Zamkovaya et al 2021 in ISME and I am excited to implement a similar network analysis (mdmnets package) with my data, but I am running into issues at the start of …
dvc28 updated
2 years ago
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Hello all,
I am currently trying to import OTU tables so I can create a phyloseq object. I have done the following (apologizes for the rather roundabout and probably redundant codes, I'm not very g…