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Composite protocol: cross-study meta-analysis of a host covariate in curatedMetagenomicData
advancedAssumes statistical or methods backgroundAssumes statistical or methods backgroundblockedWaiting on component protocols to merge firstWaiting on component protocols to merge firstcomposite-protocolComposes other protocols; adds no steps of its ownComposes other protocols; adds no steps of its ownmicrobiomeMicrobiome subject matterMicrobiome subject matterstatisticsInferential or descriptive statistical methodInferential or descriptive statistical methodStatus: Open.#34 In waldronlab/agent-protocols;Protocol: ANOSIM on a community distance matrix
atomic-protocolOne method, one citationOne method, one citationmicrobiomeMicrobiome subject matterMicrobiome subject matterstatisticsInferential or descriptive statistical methodInferential or descriptive statistical methodStatus: Open.#33 In waldronlab/agent-protocols;Protocol: PERMANOVA on a community distance matrix
atomic-protocolOne method, one citationOne method, one citationmicrobiomeMicrobiome subject matterMicrobiome subject matterstatisticsInferential or descriptive statistical methodInferential or descriptive statistical methodStatus: Open.#32 In waldronlab/agent-protocols;Protocol: random forest classification of microbiome profiles
atomic-protocolOne method, one citationOne method, one citationmachine-learningPrediction and benchmarkingPrediction and benchmarkingmicrobiomeMicrobiome subject matterMicrobiome subject matterStatus: Open.#31 In waldronlab/agent-protocols;Protocol: leave-one-dataset-out cross-study validation
atomic-protocolOne method, one citationOne method, one citationmachine-learningPrediction and benchmarkingPrediction and benchmarkingstatisticsInferential or descriptive statistical methodInferential or descriptive statistical methodStatus: Open.#30 In waldronlab/agent-protocols;Protocol: derive a reference species set for a body site or sample group by prevalence
atomic-protocolOne method, one citationOne method, one citationdata-curationCuration, cohort assembly, data preparationCuration, cohort assembly, data preparationmicrobiomeMicrobiome subject matterMicrobiome subject matterStatus: Open.#29 In waldronlab/agent-protocols;Protocol: compute the oral-to-gut enrichment score for new samples
atomic-protocolOne method, one citationOne method, one citationbioinformaticsData processing and pipelinesData processing and pipelinesmicrobiomeMicrobiome subject matterMicrobiome subject matterStatus: Open.#28 In waldronlab/agent-protocols;Protocol: two-stage hierarchical meta-analysis across diseases
advancedAssumes statistical or methods backgroundAssumes statistical or methods backgroundblockedWaiting on component protocols to merge firstWaiting on component protocols to merge firstcomposite-protocolComposes other protocols; adds no steps of its ownComposes other protocols; adds no steps of its ownstatisticsInferential or descriptive statistical methodInferential or descriptive statistical methodStatus: Open.#27 In waldronlab/agent-protocols;Protocol: random-effects meta-analysis with the Paule-Mandel heterogeneity estimator
advancedAssumes statistical or methods backgroundAssumes statistical or methods backgroundatomic-protocolOne method, one citationOne method, one citationstatisticsInferential or descriptive statistical methodInferential or descriptive statistical methodStatus: Open.#26 In waldronlab/agent-protocols;Protocol: Fisher-Z transformed partial correlations for continuous exposures
advancedAssumes statistical or methods backgroundAssumes statistical or methods backgroundatomic-protocolOne method, one citationOne method, one citationmicrobiomeMicrobiome subject matterMicrobiome subject matterstatisticsInferential or descriptive statistical methodInferential or descriptive statistical methodStatus: Open.#25 In waldronlab/agent-protocols;Protocol: per-dataset covariate-adjusted effect sizes (standardized mean difference)
advancedAssumes statistical or methods backgroundAssumes statistical or methods backgroundatomic-protocolOne method, one citationOne method, one citationmicrobiomeMicrobiome subject matterMicrobiome subject matterstatisticsInferential or descriptive statistical methodInferential or descriptive statistical methodStatus: Open.#24 In waldronlab/agent-protocols;Protocol: centred log-ratio transformation of compositional abundances
atomic-protocolOne method, one citationOne method, one citationbioinformaticsData processing and pipelinesData processing and pipelinesmicrobiomeMicrobiome subject matterMicrobiome subject matterstatisticsInferential or descriptive statistical methodInferential or descriptive statistical methodStatus: Open.#23 In waldronlab/agent-protocols;