lefser

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I have created the attached summarized experiment for analysis, but keep getting the following errors when I try to run lefser. I have followed the tutorial for creating the summarized...

dannynielsen0

Different results in lefser and LEfSe?

1

Hi, Our lab frequently run microbiome analysis using the LEfSe software from the Huttenhower lab and it would be really practical to run this analysis in R! However, when I...

CarolineWasen

If I have phyloseq file instead of example data how I show start

5

Hi Guys So I am new to lefse analysis, I start using lefser I am starting with phyloseq file then I produced otutable and with a metadata file I made...

Hesham999666

Group in lefserPlot does not reflect levels in groupCol factor

2

Hi, I'm using the vignette as an example. res

Jorisvansteenbrugge

Comparison of more than two groups

1

Hi! Great to be able to run LefSe in R - thanks! The R implementation doesn't seem to allow a comparison of more than two groups. Is there a plan...

anapopov

Test data to summarisedExperiment

4

Hi, I'm looking to implement this analyses on a dataset that i have. However, it is unclear how you went from, say a table of count data and metadata to...

susheelbhanu

Requires >= R 4.0, but not available for R version 4.0.0?

2

What am I missing? Thanks. > BiocManager::install("lefser") Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24) Installing package(s) 'lefser' Warning message: package ‘lefser’ is not available (for R version 4.0.0) >...

morganx

How to set LDA score cutoff and Kruskal-Wallis p-value cutoff?

3

Analyses using LEfSE usually state an LDA score cutoff and a Kruskal-Wallis p-value cutoff. I can see how the LDA score cutoff is possible through manual filtering of the lefserAnalysis...

lwaldron

vignette not building

1

See: https://github.com/waldronlab/lefser/runs/1078939897#step:8:12 ``` * creating vignettes ... ERROR --- re-building ‘lefser.Rmd’ using rmarkdown Quitting from lines 66-68 (lefser.Rmd) Error: processing vignette 'lefser.Rmd' failed with diagnostics: Group classification is not binary:...

lwaldron

If not assigned, lefserAnalysis gives the following error (which is good): ``` Error in EnrichmentBrowser:::.extractInfoFromSE(se) : Group assignment must be specified ``` But there needs to be documentation in `?lefserAnalysis`...

lwaldron