yiluheihei / microbiomeMarker

R package for microbiome biomarker discovery

https://yiluheihei.github.io/microbiomeMarker

yiluheihei/microbiomeMarker Issues

error in plot_cladogram function "TRUE/FALSE needed"
Updated 3 months ago
microbiomeMarker installation
Updated 4 months ago
lefse analysis error
Updated 4 months ago
Multiple errors when following tutorial using my own dataset
Updated 5 months ago
function or argument to subset taxa for plot_cladogram
Updated 6 months ago1
When run run_lefse, get different results at species level using taxa_rank default and taxa_rank="species" seperatly
Updated 6 months ago
error with run_lefse with 1 group and one subgroup: Error in `purrr::map2_lgl()`: i In index: 1
Updated 6 months ago
otu_table from run_lefse differs from otu_table from phyloseq
Closed 8 months ago1
DESeq2
Updated 8 months ago
a
Updated 8 months ago
is there a way to calculate AUC confidence interval while running run_sl
Updated 8 months ago
Error in check_rank_names(ps) : ranks of taxonimic profile must be one of Kingdom, Phylum, Class, Order, Family, Genus, Species
Updated 9 months ago1
Error in seq_len(nrow(lefse_out)) : argument must be coercible to non-negative integer
Updated 10 months ago1
suggestion: PINA and TINA
Updated a year ago
after run_lefse, plot_cladogram error
Updated a year ago2
The results of conda lefse and R run_lefse are different.
Updated a year ago1
Applying the run_lefse command.
Updated a year ago3
how to interpret the result of plot_abundance
Updated a year ago
problems importing qiime2 files
Updated a year ago1
Heatmap of microbiomeMarker object
Updated a year ago
No marker identified using run_ancombc() example
Updated a year ago1
how to import file with metaphlan2 style
Updated a year ago3
Error in run_test_multiple_groups function
Updated a year ago
plot_ef_bar() legend
Updated a year ago
import picrust2 failed: "cannot open compressed file"
Updated a year ago1
trying to normalize the microbial abundance data for beta diversity
Updated a year ago
How to choose markers identified by different methods
Updated a year ago
import the picrust output
Updated a year ago
lefse for pairwise testing while having more than 2 groups?
Updated 2 years ago
plot_ef_bar() left and right sided bars
Updated 2 years ago1
ANCOM_BC2 error: duplicate 'row.names' are not allowed
Updated 2 years ago
Error in compare_DA: Component taxa/OTU names do not match.
Updated 2 years ago
run_lefse and missing data handling
Updated 2 years ago
about function "run_test_tow_groups"
Updated 2 years ago
From phyloseq-object to microbiomemarker-class-object
Closed 2 years ago1
picrust2_import with system.file
Updated 2 years ago
how to run_lefse with subgroups and graphing them with plot_ef_bar???
Updated 2 years ago
issues installing from bioconductor
Closed 2 years ago4
Allow giving a physeq object with an ASV column
Closed 2 years ago6
Random effect syntax e.g. using `run_ancom`
Updated 2 years ago3
error in import_qiime2()
Updated 2 years ago1
the script doesn't return any output
Updated 2 years ago1
more than one taxa_rank but not "all" option?
Closed 2 years ago1
how markers were identified at Genus level while their corresponding phylum wasn't identified?
Closed 2 years ago1
Why same LEfSe object gives different taxa in Cladogram and LDA BarPlot?
Closed 2 years ago1
A way to select description for trait
Closed 2 years ago2
what is the difference bet genus with and without _g_?
Closed 2 years ago1
Plot_ef_bar() returns error for run_aldex() results
Updated 2 years ago4
contrast for multiple groups (edgeR)
Closed 2 years ago1
multigrp_strat TRUE or FALSE?
Closed 2 years ago1