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Hi,
I am quite new to microbiome analysis and, frankly, quite at a loss as to how to proceed. So, I apologize is my question is naive or has already been answered elsewhere. I have just read a paper …
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How to implement SummarizedExperiment class?
1) we can create a function for creating SummarizedExperiment based on feature counts and sample metadata, see below.
2) Should SummarizedExperiment func…
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Hello,
I finally got through the scripts to the point where I am trying to tweak my Log2FC heat.tree
I get a tree with no issues if I use the following script
set.seed(1)
obj6 %>%
heat_tree(…
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How do you decide which taxa are reported in the differential ranking? Are the differentials that are reported the coefficients that are the most changing, or those that are significant, or some combi…
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Hello team
I would like to split my dataset by condition and annotate the cell types using SingleR. Is there a way to visualize or compare the differences in cell type annotations between the two con…
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Hi everyone,
I wonder if any of you could help me to solve this problem. I have different sets of plant tissues with different treatments and I need to calculate the indicator species upon a specific…
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Can the results be presented in other ways? such like a Manhattan plot?
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Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age
https://pubmed.ncbi.nlm.nih.gov/33789672/
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```
biocbuild@kunpeng1 ~/git> R CMD check benchdamic_1.5.2.tar.gz
* using log directory ‘/home/biocbuild/git/benchdamic.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using …
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Hi!
I am working to replicate your perturbation prediction result. A little clarity as to the method would be helpful.
For this task was a model finetuned on the distinct task "reverse pertur…