Tests which individual taxa differ between groups on an amplicon ASV/feature table (phyloseq) using compositionally-aware methods - ALDEx2 (Dirichlet-MC CLR, conservative), ANCOM-BC2/ANCOMBC (sampling-fraction bias correction, structural zeros, passedss, default padjmethod=holm), MaAsLin2/MaAsLin3 (multivariable GLM, random effects, prevalence/abundance split), LinDA (CLR mixed-model regression), ZicoSeq (permutation FDR), LEfSe, and q2-composition ancombc. Covers why the hit list depends more on the DA tool than the biology (Nearing benchmark) so the deliverable is a CONSENSUS of >=2 tools, why a relative change is not absolute without a load anchor, the prevalence-filter knob, BH/FDR plus an effect-size floor, and why DESeq2/edgeR misfire here. Use when finding differentially abundant taxa, handling covariates or longitudinal designs, or choosing a method. Whole-community diversity -> diversity-analysis; shotgun DA -> metagenomics/metagenome-visualization; CoDA theory -> metagenomics/abundance-estimation
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Claude CodeCodexCursorGitHub CopilotGemini CLI
Supported by the Atlas install prompt. Skill-specific requirements vary.
Skill stats
Skills1CategoryScience & researchStars0
About this skill
Tests which individual taxa differ between groups on an amplicon ASV/feature table (phyloseq) using compositionally-aware methods - ALDEx2 (Dirichlet-MC CLR, conservative), ANCOM-BC2/ANCOMBC (sampling-fraction bias correction, structural zeros, passedss, default padjmethod=holm), MaAsLin2/MaAsLin3 (multivariable GLM, random effects, prevalence/abundance split), LinDA (CLR mixed-model regression), ZicoSeq (permutation FDR), LEfSe, and q2-composition ancombc. Covers why the hit list depends more on the DA tool than the biology (Nearing benchmark) so the deliverable is a CONSENSUS of >=2 tools, why a relative change is not absolute without a load anchor, the prevalence-filter knob, BH/FDR plus an effect-size floor, and why DESeq2/edgeR misfire here. Use when finding differentially abundant taxa, handling covariates or longitudinal designs, or choosing a method. Whole-community diversity -> diversity-analysis; shotgun DA -> metagenomics/metagenome-visualization; CoDA theory -> metagenomics/abundance-estimation
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Tests which individual taxa differ between groups on an amplicon ASV/feature table (phyloseq) using compositionally-aware methods - ALDEx2 (Dirichlet-MC CLR, conservative), ANCOM-BC2/ANCOMBC (sampling-fraction bias correction, structural zeros, passed_ss, default p_adj_method=holm), MaAsLin2/MaAsLin3 (multivariable GLM, random effects, prevalence/abundance split), LinDA (CLR mixed-model regression), ZicoSeq (permutation FDR), LEfSe, and q2-composition ancombc. Covers why the hit list depends more on the DA tool than the biology (Nearing benchmark) so the deliverable is a CONSENSUS of >=2 tools, why a relative change is not absolute without a load anchor, the prevalence-filter knob, BH/FDR plus an effect-size floor, and why DESeq2/edgeR misfire here. Use when finding differentially abundant taxa, handling covariates or longitudinal designs, or choosing a method. Whole-community diversity -> diversity-analysis; shotgun DA -> metagenomics/metagenome-visualization; CoDA theory -> metagenomics/abundance-estimation
About this listing
Category
Science & research
Reported license
Not specified
Listing language (estimated)
English
Review status
Not individually reviewed
Agent compatibility
Atlas installation supports Claude Code, Codex, and Cursor. Skill-specific dependencies and features are checked during setup.
Claude Code
Codex
Cursor
GitHub Copilot
Gemini CLI