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Question on Running HUMAnN4 with Limited Memory on HPC
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3
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167
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August 1, 2025
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Question Regarding the Use of MaAsLin3 for Analyzing Differential Abundance/Prevalence of MetaCyc and GMM Metabolic Pathways
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4
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161
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November 4, 2025
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Problems running Humann
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2
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106
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September 25, 2025
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Prevotella copri clades in MetaPhlAn 4 results
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5
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79
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September 22, 2025
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Maaslin Analysis with Non-clinical data and Small samples
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5
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132
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October 7, 2025
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Discrepancy Between Input Reads and Estimated Read Counts in MetaPhlAn 4
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3
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145
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July 10, 2025
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MetaPhlAn 4.2.2 --profile_vsc
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4
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127
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September 12, 2025
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Very low mapping rate of Hummann v4alpha
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3
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138
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March 6, 2026
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Association between microbiome feature and next timepoint outcome
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1
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36
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December 15, 2025
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Error encountered when using hclust2.py in the conda-created metaphlan4.2.2 environment on Ubuntu 22 terminal
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0
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51
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October 15, 2025
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Metaphlan: sgb_to_gtdb_profile.py fails with KeyError
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3
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142
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October 27, 2025
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Strainphlan sample2markers.py ERROR
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5
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122
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December 18, 2025
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Metaphlan: error: unrecognized arguments: --bowtie2db
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1
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182
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July 2, 2025
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HUMAnN 4.0.0.alpha.1 calls "old" metaphlan command-line args
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1
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199
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June 30, 2025
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Dereplicating and normalizing reads for humann and metaphlan
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6
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102
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January 30, 2026
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Presence of fungi in ChocoPhlAn vJan25
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1
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106
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October 30, 2025
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Maaslin3 error message
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5
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101
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February 12, 2026
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ERROR: The MetaPhlAn taxonomic profile provided was not generated with the expected database version. Please update your version of MetaPhlAn to at least v3.0
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1
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169
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September 25, 2025
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Errors with humann-metaphlan
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2
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162
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September 23, 2025
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Pseudocount application in Maaslin2 vs Maaslin3
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2
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144
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June 2, 2025
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Suggested min_prevalence and min_abundances for mataphlan or humann inputs in maaslin
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3
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121
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September 5, 2025
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Can't install MelonnPan -- AssocTests no longer available
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5
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118
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October 15, 2025
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Metaphlan --install deletes minimap fasta
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2
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134
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October 29, 2025
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How should I compare HUMAnN 4 “Counts” from concatenated paired-end reads to known species read abundances?
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3
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121
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November 6, 2025
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Baqlava marker file has markers not seen in the profile
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1
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59
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June 20, 2025
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Strain taxonomic level Identification
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2
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122
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April 2, 2026
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Batch correction for microbiome data
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0
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243
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May 29, 2025
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Error when running HUMAnN tutorial
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2
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158
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July 25, 2025
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Combine metaphlan and humann
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2
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126
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June 15, 2025
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Unable to download the databases in Humann4
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1
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152
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November 4, 2025
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Understanding Fixed Effects in Maaslin3 Microbiome Analysis
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1
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149
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July 18, 2025
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MetaPhlAn Databases
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1
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138
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June 13, 2025
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Maaslin3 summary plot
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1
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146
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June 7, 2025
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LEfSe via galaxy
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1
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138
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June 16, 2025
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Can I use the option --bowtie2out (for StrainPhlan!) along HUMANn?
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3
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104
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May 29, 2025
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READS_UNMAPPED Is Not Presented in CPM Format
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2
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135
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February 18, 2026
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Question about 'baselines' for effects Maaslin3
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8
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76
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January 23, 2026
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HUMAnN 3.0 stratified KOs return paradoxical interpretations
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1
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76
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December 4, 2025
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Error message Maaslin3
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3
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98
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June 18, 2025
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Explaining meaning of maaslin3 error messages
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2
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116
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October 3, 2025
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Total RNA contribution for Metatranscriptomics Analysis with MaAsLin3
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5
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80
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November 8, 2025
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Calculate alpha diversity before or after filtering?
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1
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139
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July 17, 2025
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HUMAnN pathway coverage: community total ≪ species coverage. Why can this happen?
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2
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115
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August 27, 2025
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Rarecurve on long read from Metaphlan 4.2.2
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3
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96
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October 27, 2025
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HUMAnN installs for Python 3.12 in a Python 3.13 environment
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1
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134
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August 27, 2025
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MaAsLin2: Comparing results with one fixed effect vs many
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1
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127
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June 18, 2025
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HUMAnN targeted functional analysis?
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2
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106
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January 9, 2026
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MetaPhlAn v4.2.3 installation errors
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2
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101
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October 20, 2025
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Metaphlan Results Interpretation
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2
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103
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November 5, 2025
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Error: <ggplot2::labels> object is invalid:
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1
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125
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December 16, 2025
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