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Hello,
I am using the Lefse on google golab by pytnon 2.7 based on the following command lines;
!conda install -c biobakery lefse
!format_input.py hmp_aerobiosis_small.txt hmp_aerobiosis_small…
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While running the command for phyloseq_to_lefse I am getting an output of the below attached file. It cannot work in Galaxy . Kindly help ..
[lefse_Rev.txt](https://github.com/seashore001x/Rrumen/f…
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Dear All,
I have a bit problem with the LESFE analysis starting from a phyloseq object.
I tried to use the LEFSE package from ying14/yingtools2: Ying's R Tools, following the exemple code.
Belo…
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This is a new warning being generated by the tests, and I don't think there are actually should be collinear variables here so I'm not sure what's happening.
``` r
suppressPackageStartupMessages(l…
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Hi
When I ran the code to calculate LEFSE, it showed error as below
> feature_table sample_table tax_table dataset dataset
microtable-class object:
sample_table have 5 rows and 3 columns
ot…
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Are there any way to customize the plots lefse generates (with labels)? The autogenerated plots doesn't have labels and are of low resolution.
Any help would be appreciated!
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Hello!
I'm currently facing an issue while using LEfSe. Specifically, when attempting the first step A) Format Data for LEfSe with the example file hmp_aerobiosis_small.txt, I encounter an error th…
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MacQIIME Todds-Mac-Pro:qiime_to_lefse-master $ python qiime_to_lefse.py -m map_soil_final3.txt -t soil_phyloseq_json_L6.txt -c Description -o converted_2lefse.txt --clean
Traceback (most recent call…
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Using the Phyloseq object, after run_lefse, plot_ef_bar was normally derived.
However, plot_cladogram or microbiomeMarker::plot_cladogram
causes the following problem:
command
microbiomeMarker…