FelixErnst/mia
Microbiome analysis

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Source code
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Man pages
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FelixErnst/mia: Microbiome analysis
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API

API for FelixErnst/mia
Microbiome analysis

Global functions
.JSD Source code
.add_coldata Source code
.add_object_to_reduceddim Source code
.add_row_data_to_molten_assay Source code
.add_rowdata_to_rownames Source code
.add_taxonomic_type Source code
.add_to_altExps Source code
.add_to_coldata Source code
.add_trees Source code
.add_values_to_colData Source code
.add_values_to_metadata Source code
.add_values_to_reducedDims Source code
.adjust_alr_table Source code
.agg_for_prevalence Source code
.agglomerate_trees Source code
.all_are_existing_files Source code
.alpha_rarefaction Source code
.apply_pseudocount Source code
.apply_transformation Source code
.apply_transformation_from_vegan Source code
.are_whole_numbers Source code
.assay_cannot_be_found Source code
.assays_cannot_be_found Source code
.association_filter Source code
.association_sort Source code
.association_table_to_matrix Source code
.calc_ace Source code
.calc_bulla_evenness Source code
.calc_camargo_evenness Source code
.calc_chao1 Source code
.calc_core_dominance Source code
.calc_coverage Source code
.calc_css Source code
.calc_css_percentile Source code
.calc_divergence Source code
.calc_dominance Source code
.calc_evar_evenness Source code
.calc_faith Source code
.calc_fisher Source code
.calc_gini_dominance Source code
.calc_gini_simpson Source code
.calc_hill Source code
.calc_inverse_simpson Source code
.calc_log Source code
.calc_log_modulo_skewness Source code
.calc_observed Source code
.calc_pielou_evenness Source code
.calc_rel_abund Source code
.calc_scaling_factors Source code
.calc_shannon Source code
.calc_simpson_evenness Source code
.calc_skewness Source code
.calculate_DMN Source code
.calculate_DMNgroup Source code
.calculate_association Source code
.calculate_association_for_categorical_values Source code
.calculate_association_for_numeric_values Source code
.calculate_association_table Source code
.calculate_association_with_own_function Source code
.calculate_dissimilarity Source code
.calculate_dpcoa Source code
.calculate_gktau Source code
.calculate_lda_metrics Source code
.calculate_nmds Source code
.calculate_rda Source code
.calculate_stats_cor Source code
.capitalize Source code
.check.mediate.args Source code
.check_MARGIN Source code
.check_NAs_assay_counts Source code
.check_altExp_present Source code
.check_and_add_refSeqs Source code
.check_and_add_trees Source code
.check_and_get_altExp Source code
.check_and_subset_colData_variables Source code
.check_assay_present Source code
.check_assays_for_merge Source code
.check_colTree_present Source code
.check_dimnames Source code
.check_for_taxonomic_data_order Source code
.check_fraction_or_negative_values Source code
.check_if_paired_samples Source code
.check_max_taxa Source code
.check_metaphlan Source code
.check_object_for_merge Source code
.check_objects_and_give_class Source code
.check_rowTree_present Source code
.check_taxonomic_rank Source code
.check_taxonomic_ranks Source code
.check_that_assays_match Source code
.combine_assays Source code
.combine_colData Source code
.combine_rowData Source code
.combine_rowRanges Source code
.convert_se_to_biom Source code
.create_biom Source code
.create_row_data Source code
.create_se_from_metaphlan Source code
.create_tse_from_humann Source code
.cross_association_test_data_type Source code
.detect_taxa_artifacts_and_clean Source code
.estimate_diversity Source code
.estimate_dominance Source code
.estimate_evenness Source code
.estimate_faith Source code
.estimate_richness Source code
.format_molten_assay Source code
.format_nmds Source code
.format_nmds_isoMDS Source code
.format_nmds_monoMDS Source code
.get_SummarizedExperiment_data Source code
.get_TreeSE_args Source code
.get_assay Source code
.get_best_dmn_fit Source code
.get_best_nmf_fit Source code
.get_diversity_values Source code
.get_dmn Source code
.get_dmn_fit_FUN Source code
.get_dominance_values Source code
.get_element_pos Source code
.get_empty_nodes Source code
.get_evenness_values Source code
.get_experiment_cross_association Source code
.get_ext Source code
.get_formula_and_covariates Source code
.get_indices Source code
.get_jsd Source code
.get_lowest_taxonomic_level Source code
.get_map_result Source code
.get_matrix_and_reference Source code
.get_name_in_parent Source code
.get_nmds_args Source code
.get_nmds_args_isoMDS Source code
.get_nmds_args_monoMDS Source code
.get_overlap Source code
.get_prevalent_indices Source code
.get_prevalent_taxa Source code
.get_ranks Source code
.get_rare_indices Source code
.get_rare_taxa Source code
.get_referenceSeq_for_phyloseq Source code
.get_reference_type Source code
.get_richness_values Source code
.get_rowTree_for_phyloseq Source code
.get_singletons Source code
.get_subset_args Source code
.get_summary_col_data Source code
.get_summary_row_data Source code
.get_tax_cols Source code
.get_tax_cols_from_se Source code
.get_tax_cols_logical Source code
.get_tax_groups Source code
.get_tax_ranks_selected Source code
.get_taxa_any_match Source code
.get_taxa_row_match Source code
.get_taxonomic_label Source code
.get_tips_to_drop Source code
.get_tree_args Source code
.get_tree_args_from_TreeSE Source code
.get_unifrac Source code
.get_unique_names Source code
.get_variables_based_on_formula Source code
.get_x_with_pruned_tree Source code
.gini_dominance Source code
.homogeneity_significance Source code
.idtaxa_to_DataFrame Source code
.is_a_bool Source code
.is_a_numeric Source code
.is_a_string Source code
.is_an_integer Source code
.is_function Source code
.is_integer Source code
.is_mothur_constaxonomy_file Source code
.is_mothur_design_file Source code
.is_mothur_shared_file Source code
.is_mothur_taxonomy_file Source code
.is_non_empty_character Source code
.is_non_empty_string Source code
.is_numeric_string Source code
.join_two_tables Source code
.list_unsplit_on Source code
.make.output Source code
.melt_assay Source code
.merge_SEs Source code
.merge_SummarizedExperiments Source code
.merge_assay Source code
.merge_assay_by_rows Source code
.merge_coldata Source code
.merge_cols Source code
.merge_cols_TSE Source code
.merge_features Source code
.merge_refseq Source code
.merge_refseq_list Source code
.merge_rowdata Source code
.merge_rows Source code
.merge_rows_TSE Source code
.merge_trees Source code
.norm_add_row_data Source code
.norm_archetype Source code
.norm_args_for_split_by Source code
.norm_args_for_split_by_ranks Source code
.norm_f Source code
.norm_rownames Source code
.onAttach Source code
.order_based_on_trees Source code
.parse_metaphlan Source code
.parse_taxonomy Source code
.perform_DMNgroup_cv Source code
.prune_tree Source code
.read_humann Source code
.read_metaphlan Source code
.read_mothur_feature Source code
.read_mothur_sample_meta Source code
.read_mothur_taxonomy Source code
.read_q2biom Source code
.read_q2sample_meta Source code
.read_q2taxa Source code
.remove_NA_cols_from_rowdata Source code
.remove_NAs_and_sort Source code
.remove_prefixes_from_taxa Source code
.remove_special_functions_from_terms Source code
.remove_suffix Source code
.remove_with_empty_taxonomic_info Source code
.rename_based_on_samplemap Source code
.replace_colnames_based_on_prefix Source code
.require_package Source code
.rownames_as_dna_seq Source code
.run.mediate Source code
.set_feature_tab_dimnames Source code
.set_ranks_based_on_rowdata Source code
.simpson_lambda Source code
.sort_variable_pairs_row_wise Source code
.split_by_ranks Source code
.split_on Source code
.subsample_assay Source code
.subset_taxa_in_feature Source code
.tally_col_data Source code
.test_experiment_of_mae Source code
.test_rda Source code
.test_rda_vars Source code
.to_rel_abund Source code
.top_n Source code
.transform_assay Source code
.unsplit_assays Source code
.unsplit_by Source code
.unsplit_by_ranks Source code
.update.results Source code
GlobalPatterns Man page
HintikkaXOData Man page
IdTaxaToDataFrame Man page
Tengeler2020 Man page
Tito2024QMP Man page
ZTransform Man page
ZTransform,SummarizedExperiment-method Man page
addAlpha Man page
addAlpha,SummarizedExperiment-method Man page
addCCA Man page
addCCA,SingleCellExperiment-method Man page
addCluster Man page
addCluster,SummarizedExperiment-method Man page
addContaminantQC Man page
addContaminantQC,SummarizedExperiment-method Man page
addDPCoA Man page Source code
addDissimilarity Man page
addDissimilarity,SummarizedExperiment-method Man page
addDivergence Man page
addDivergence,SummarizedExperiment-method Man page
addDominant Man page
addDominant,SummarizedExperiment-method Man page
addHierarchyTree Man page
addHierarchyTree,SummarizedExperiment-method Man page
addLDA Man page
addLDA,SummarizedExperiment-method Man page
addMediation Man page
addMediation,SummarizedExperiment-method Man page
addNMDS Man page Source code
addNMF Man page
addNMF,SummarizedExperiment-method Man page
addNotContaminantQC Man page
addNotContaminantQC,SummarizedExperiment-method Man page
addPerSampleDominantFeatures Man page
addPerSampleDominantFeatures,SummarizedExperiment-method Man page
addPerSampleDominantTaxa Man page
addPerSampleDominantTaxa,SummarizedExperiment-method Man page
addRDA Man page
addRDA,SingleCellExperiment-method Man page
addTaxonomyTree Man page
addTaxonomyTree,SummarizedExperiment-method Man page
agglomerate-methods Man page
agglomerateByPrevalence Man page
agglomerateByPrevalence,SummarizedExperiment-method Man page
agglomerateByPrevalence,TreeSummarizedExperiment-method Man page
agglomerateByRank Man page
agglomerateByRank,SingleCellExperiment-method Man page
agglomerateByRank,SummarizedExperiment-method Man page
agglomerateByRank,TreeSummarizedExperiment-method Man page
agglomerateByRanks Man page
agglomerateByRanks,SingleCellExperiment-method Man page
agglomerateByRanks,SummarizedExperiment-method Man page
agglomerateByRanks,TreeSummarizedExperiment-method Man page
agglomerateByVariable Man page
agglomerateByVariable,SummarizedExperiment-method Man page
agglomerateByVariable,TreeSummarizedExperiment-method Man page
bestDMNFit Man page
bestDMNFit,SummarizedExperiment-method Man page
calculateCCA Man page Source code
calculateDMN Man page
calculateDMN,ANY-method Man page
calculateDMN,SummarizedExperiment-method Man page
calculateDMNgroup Man page
calculateDMNgroup,ANY-method Man page
calculateDMNgroup,SummarizedExperiment-method Man page
calculateDPCoA Man page Source code
calculateJSD Man page
calculateJSD,ANY-method Man page
calculateNMDS Man page Source code
calculateOverlap Man page
calculateOverlap,ANY-method Man page
calculateRDA Man page Source code
calculateUnifrac Man page
calculateUnifrac,ANY-method Man page
checkTaxonomy Man page
checkTaxonomy,SummarizedExperiment-method Man page
cluster Man page
cluster,SummarizedExperiment-method Man page
convertFromBIOM Man page Source code
convertFromDADA2 Man page Source code
convertFromPhyloseq Man page Source code
convertToBIOM Man page
convertToBIOM,SummarizedExperiment-method Man page
convertToPhyloseq Man page
convertToPhyloseq,SummarizedExperiment-method Man page
convertToPhyloseq,TreeSummarizedExperiment-method Man page
countDominantFeatures Man page
countDominantFeatures,SummarizedExperiment-method Man page
countDominantTaxa Man page
countDominantTaxa,SummarizedExperiment-method Man page
deprecate Man page
dmn_se Man page
enterotype Man page
esophagus Man page
estimateDivergence Man page
estimateDivergence,SummarizedExperiment-method Man page
estimateDiversity Man page
estimateDiversity,ANY-method Man page
estimateDominance Man page
estimateDominance,ANY-method Man page
estimateEvenness Man page
estimateEvenness,ANY-method Man page
estimateFaith Man page
estimateFaith,ANY-method Man page
estimateRichness Man page
estimateRichness,ANY-method Man page
full_join Man page
full_join,ANY-method Man page
getBestDMNFit Man page
getBestDMNFit,SummarizedExperiment-method Man page
getCCA Man page
getCCA,ANY-method Man page
getCCA,SummarizedExperiment-method Man page
getCrossAssociation Man page
getCrossAssociation,MultiAssayExperiment-method Man page
getCrossAssociation,SummarizedExperiment-method Man page
getDMN Man page
getDMN,SummarizedExperiment-method Man page
getDPCoA Man page
getDPCoA,ANY,ANY-method Man page
getDPCoA,TreeSummarizedExperiment,missing-method Man page
getDissimilarity Man page
getDissimilarity,ANY-method Man page
getDissimilarity,SummarizedExperiment-method Man page
getDissimilarity,TreeSummarizedExperiment-method Man page
getDivergence Man page
getDivergence,SummarizedExperiment-method Man page
getDominant Man page
getDominant,SummarizedExperiment-method Man page
getExperimentCrossAssociation Man page
getExperimentCrossAssociation,MultiAssayExperiment-method Man page
getExperimentCrossAssociation,SummarizedExperiment-method Man page
getExperimentCrossCorrelation Man page
getExperimentCrossCorrelation,ANY-method Man page
getHierarchyTree Man page
getHierarchyTree,SummarizedExperiment-method Man page
getLDA Man page
getLDA,SummarizedExperiment-method Man page
getMediation Man page
getMediation,SummarizedExperiment-method Man page
getNMDS Man page
getNMDS,ANY-method Man page
getNMDS,SingleCellExperiment-method Man page
getNMDS,SummarizedExperiment-method Man page
getNMF Man page
getNMF,SummarizedExperiment-method Man page
getPrevalence Man page
getPrevalence,ANY-method Man page
getPrevalence,SummarizedExperiment-method Man page
getPrevalent Man page
getPrevalent,ANY-method Man page
getPrevalent,SummarizedExperiment-method Man page
getPrevalentAbundance Man page
getPrevalentAbundance,ANY-method Man page
getPrevalentAbundance,SummarizedExperiment-method Man page
getPrevalentFeatures Man page
getPrevalentFeatures,ANY-method Man page
getPrevalentFeatures,SummarizedExperiment-method Man page
getPrevalentTaxa Man page
getPrevalentTaxa,ANY-method Man page
getPrevalentTaxa,SummarizedExperiment-method Man page
getRDA Man page
getRDA,ANY-method Man page
getRDA,SummarizedExperiment-method Man page
getRare Man page
getRare,ANY-method Man page
getRare,SummarizedExperiment-method Man page
getRareFeatures Man page
getRareFeatures,ANY-method Man page
getRareFeatures,SummarizedExperiment-method Man page
getRareTaxa Man page
getRareTaxa,ANY-method Man page
getRareTaxa,SummarizedExperiment-method Man page
getTaxonomyLabels Man page
getTaxonomyLabels,SummarizedExperiment-method Man page
getTaxonomyRankPrefixes Source code
getTaxonomyRanks Man page Source code
getTop Man page
getTop,SummarizedExperiment-method Man page
getTopFeatures Man page
getTopFeatures,SummarizedExperiment-method Man page
getTopTaxa Man page
getTopTaxa,SummarizedExperiment-method Man page
getUnique Man page
getUnique,SummarizedExperiment-method Man page
getUniqueFeatures Man page
getUniqueFeatures,SummarizedExperiment-method Man page
getUniqueTaxa Man page
getUniqueTaxa,SummarizedExperiment-method Man page
hierarchy-tree Man page
importBIOM Man page Source code
importHUMAnN Man page Source code
importMetaPhlAn Man page Source code
importMothur Man page Source code
importQIIME2 Man page Source code
importQZA Man page Source code
importTaxpasta Man page Source code
inner_join Man page
inner_join,ANY-method Man page
isContaminant Man page
isContaminant,SummarizedExperiment-method Man page
isNotContaminant,SummarizedExperiment-method Man page
left_join Man page
left_join,ANY-method Man page
loadFromBiom Man page Source code
loadFromHumann Man page Source code
loadFromMetaphlan Man page Source code
loadFromMothur Man page Source code
loadFromQIIME2 Man page Source code
makePhyloseqFromTreeSE Man page
makePhyloseqFromTreeSE,SummarizedExperiment-method Man page
makePhyloseqFromTreeSE,TreeSummarizedExperiment-method Man page
makePhyloseqFromTreeSummarizedExperiment Man page
makePhyloseqFromTreeSummarizedExperiment,ANY-method Man page
makeTreeSEFromBiom Man page Source code
makeTreeSEFromDADA2 Man page Source code
makeTreeSEFromPhyloseq Man page Source code
makeTreeSummarizedExperimentFromBiom Man page Source code
makeTreeSummarizedExperimentFromDADA2 Man page Source code
makeTreeSummarizedExperimentFromPhyloseq Man page
makeTreeSummarizedExperimentFromPhyloseq,ANY-method Man page
mapTaxonomy Man page
mapTaxonomy,SummarizedExperiment-method Man page
meltAssay Man page
meltAssay,SummarizedExperiment-method Man page
meltSE Man page
meltSE,SummarizedExperiment-method Man page
mergeCols Man page
mergeCols,SummarizedExperiment-method Man page
mergeCols,TreeSummarizedExperiment-method Man page
mergeFeatures Man page
mergeFeatures,SummarizedExperiment-method Man page
mergeFeatures,TreeSummarizedExperiment-method Man page
mergeFeaturesByPrevalence Man page
mergeFeaturesByPrevalence,SummarizedExperiment-method Man page
mergeFeaturesByRank Man page
mergeFeaturesByRank,SingleCellExperiment-method Man page
mergeFeaturesByRank,SummarizedExperiment-method Man page
mergeFeaturesByRank,TreeSummarizedExperiment-method Man page
mergeRows Man page
mergeRows,SummarizedExperiment-method Man page
mergeRows,TreeSummarizedExperiment-method Man page
mergeSEs Man page
mergeSEs,SimpleList-method Man page
mergeSEs,SummarizedExperiment-method Man page
mergeSEs,list-method Man page
mergeSamples Man page
mergeSamples,SummarizedExperiment-method Man page
mergeSamples,TreeSummarizedExperiment-method Man page
mia Man page
mia-datasets Man page
mia-package Man page
peerj13075 Man page
perSampleDominantFeatures Man page
perSampleDominantFeatures,SummarizedExperiment-method Man page
perSampleDominantTaxa Man page
perSampleDominantTaxa,SummarizedExperiment-method Man page
performDMNgroupCV Man page
performDMNgroupCV,ANY-method Man page
performDMNgroupCV,SummarizedExperiment-method Man page
plotNMDS Man page Source code
rarefyAssay Man page
rarefyAssay,SummarizedExperiment-method Man page
readQZA Man page Source code
relAbundanceCounts Man page
relAbundanceCounts,SummarizedExperiment-method Man page
relabundance Man page
relabundance,SummarizedExperiment-method Man page
relabundance<- Man page
relabundance<-,SummarizedExperiment-method Man page
right_join Man page
right_join,ANY-method Man page
runCCA Man page Source code
runDMN Man page Source code
runDPCoA Man page Source code
runJSD Man page
runJSD,SummarizedExperiment-method Man page
runNMDS Man page Source code
runOverlap Man page
runOverlap,SummarizedExperiment-method Man page
runRDA Man page Source code
runUnifrac Man page Source code
setTaxonomyRankPrefixes Source code
setTaxonomyRanks Man page Source code
splitByRanks Man page Source code
splitOn Man page
splitOn,SingleCellExperiment-method Man page
splitOn,SummarizedExperiment-method Man page
splitOn,TreeSummarizedExperiment-method Man page
subsampleCounts Man page
subsampleCounts,SummarizedExperiment-method Man page
subsetByPrevalent Man page
subsetByPrevalent,SummarizedExperiment-method Man page
subsetByPrevalentFeatures Man page
subsetByPrevalentFeatures,ANY-method Man page
subsetByPrevalentTaxa Man page
subsetByPrevalentTaxa,ANY-method Man page
subsetByRare Man page
subsetByRare,SummarizedExperiment-method Man page
subsetByRareFeatures Man page
subsetByRareFeatures,ANY-method Man page
subsetByRareTaxa Man page
subsetByRareTaxa,ANY-method Man page
subsetFeatures Man page
subsetFeatures,SummarizedExperiment-method Man page
subsetSamples Man page
subsetSamples,SummarizedExperiment-method Man page
subsetTaxa Man page
subsetTaxa,SummarizedExperiment-method Man page
summaries Man page
summarizeDominance Man page
summarizeDominance,SummarizedExperiment-method Man page
summary,SummarizedExperiment-method Man page
taxonomy-methods Man page
taxonomyRankEmpty Man page
taxonomyRankEmpty,SummarizedExperiment-method Man page
taxonomyRanks Man page
taxonomyRanks,SummarizedExperiment-method Man page
taxonomyTree Man page
taxonomyTree,SummarizedExperiment-method Man page
testExperimentCrossAssociation Man page
testExperimentCrossAssociation,ANY-method Man page
testExperimentCrossCorrelation Man page
testExperimentCrossCorrelation,ANY-method Man page
transformAssay Man page
transformAssay,SingleCellExperiment-method Man page
transformAssay,SummarizedExperiment-method Man page
transformCounts Man page Source code
transformFeatures Man page
transformFeatures,SummarizedExperiment-method Man page
transformSamples Man page
transformSamples,SummarizedExperiment-method Man page
twins Man page
unsplitByRanks Man page
unsplitByRanks,SingleCellExperiment-method Man page
unsplitByRanks,TreeSummarizedExperiment-method Man page
unsplitOn Man page
unsplitOn,SimpleList-method Man page
unsplitOn,SingleCellExperiment-method Man page
unsplitOn,list-method Man page
FelixErnst/mia documentation built on Nov. 3, 2024, 2:51 a.m.

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