Index

A

Abundance (onecodex.lib.enums.FunctionalAnnotationsMetric attribute) (onecodex.lib.enums.Metric attribute), [1] AbundanceWChildren (onecodex.lib.enums.Metric attribute), [1] Aitchison (onecodex.lib.enums.BetaDiversityMetric attribute) aitchison_distance() (onecodex.models.collection.SampleCollection method) Alignments (class in onecodex.models.analysis) alpha_diversity() (onecodex.models.collection.SampleCollection method)

alpha_diversity_stats() (onecodex.models.collection.SampleCollection method) AlphaDiversityMetric (class in onecodex.lib.enums) AlphaDiversityStatsResults (class in onecodex.stats) Analyses (class in onecodex.models.analysis) Assets (class in onecodex.models.misc) Auto (onecodex.lib.enums.Metric attribute), [1] (onecodex.lib.enums.Rank attribute) Average (onecodex.lib.enums.Linkage attribute)

B

beta_diversity() (onecodex.models.collection.SampleCollection method) beta_diversity_stats() (onecodex.models.collection.SampleCollection method)

BetaDiversityMetric (class in onecodex.lib.enums) BetaDiversityStatsResults (class in onecodex.stats) BrayCurtis (onecodex.lib.enums.BetaDiversityMetric attribute)

C

Centroid (onecodex.lib.enums.Linkage attribute) Chao1 (onecodex.lib.enums.AlphaDiversityMetric attribute) CityBlock (onecodex.lib.enums.BetaDiversityMetric attribute) Class (onecodex.lib.enums.Rank attribute)

Classifications (class in onecodex.models.analysis) Complete (onecodex.lib.enums.Linkage attribute) CompleteAbundance (onecodex.lib.enums.FunctionalAnnotationsMetric attribute) Coverage (onecodex.lib.enums.FunctionalAnnotationsMetric attribute) Cpm (onecodex.lib.enums.FunctionalAnnotationsMetric attribute)

D

display_name (onecodex.lib.enums.Metric property) Documents (class in onecodex.models.misc) download_file() (onecodex.models.analysis.Alignments method) (onecodex.models.analysis.Analyses method) (onecodex.models.analysis.Classifications method) (onecodex.models.analysis.FunctionalProfiles method) (onecodex.models.analysis.Panels method)

dtype (onecodex.lib.enums.Metric property)

E

Ec (onecodex.lib.enums.FunctionalAnnotations attribute)

EggNog (onecodex.lib.enums.FunctionalAnnotations attribute) Euclidean (onecodex.lib.enums.BetaDiversityMetric attribute)

F

Family (onecodex.lib.enums.Rank attribute) filter() (onecodex.models.collection.SampleCollection method) filtered_table() (onecodex.models.analysis.FunctionalProfiles method)

FunctionalAnnotations (class in onecodex.lib.enums) FunctionalAnnotationsMetric (class in onecodex.lib.enums) FunctionalProfiles (class in onecodex.models.analysis)

G

Genus (onecodex.lib.enums.Rank attribute) get_files() (onecodex.models.analysis.Alignments method) (onecodex.models.analysis.Analyses method) (onecodex.models.analysis.Classifications method) (onecodex.models.analysis.FunctionalProfiles method) (onecodex.models.analysis.Panels method)

Go (onecodex.lib.enums.FunctionalAnnotations attribute)

I

includes_children (onecodex.lib.enums.Metric property)

is_abundance_metric (onecodex.lib.enums.Metric property) is_normalized (onecodex.lib.enums.Metric property)

J

Jaccard (onecodex.lib.enums.BetaDiversityMetric attribute)

Jobs (class in onecodex.models.misc)

K

Kingdom (onecodex.lib.enums.Rank attribute)

Ko (onecodex.lib.enums.FunctionalAnnotations attribute)

L

Linkage (class in onecodex.lib.enums)

M

Manhattan (onecodex.lib.enums.BetaDiversityMetric attribute) Median (onecodex.lib.enums.Linkage attribute) MetaCyc (onecodex.lib.enums.FunctionalAnnotations attribute) Metric (class in onecodex.lib.enums) model_config (onecodex.models.analysis.Alignments attribute) (onecodex.models.analysis.Analyses attribute) (onecodex.models.analysis.Classifications attribute) (onecodex.models.analysis.FunctionalProfiles attribute) (onecodex.models.analysis.Panels attribute) (onecodex.models.misc.Assets attribute) (onecodex.models.misc.Documents attribute) (onecodex.models.misc.Jobs attribute) (onecodex.models.misc.Projects attribute) (onecodex.models.misc.Tags attribute) (onecodex.models.misc.Users attribute) (onecodex.models.sample.Samples attribute)

N

NormalizedReadcount (onecodex.lib.enums.Metric attribute), [1]

NormalizedReadcountWChildren (onecodex.lib.enums.Metric attribute), [1]

O

ObservedTaxa (onecodex.lib.enums.AlphaDiversityMetric attribute)

Order (onecodex.lib.enums.Rank attribute) OrdinationMethod (class in onecodex.lib.enums)

P

Panels (class in onecodex.models.analysis) Pathways (onecodex.lib.enums.FunctionalAnnotations attribute) Pcoa (onecodex.lib.enums.OrdinationMethod attribute) Pfam (onecodex.lib.enums.FunctionalAnnotations attribute) Phylum (onecodex.lib.enums.Rank attribute) plot_bargraph() (onecodex.models.collection.SampleCollection method) plot_distance() (onecodex.models.collection.SampleCollection method) plot_functional_heatmap() (onecodex.models.collection.SampleCollection method) plot_heatmap() (onecodex.models.collection.SampleCollection method)

plot_mds() (onecodex.models.collection.SampleCollection method) plot_metadata() (onecodex.models.collection.SampleCollection method) plot_pca() (onecodex.models.collection.SampleCollection method) PosthocResults (class in onecodex.stats) preupload() (onecodex.models.sample.Samples class method) Projects (class in onecodex.models.misc) PropClassified (onecodex.lib.enums.Metric attribute), [1] PropClassifiedWChildren (onecodex.lib.enums.Metric attribute), [1] PropReadcount (onecodex.lib.enums.Metric attribute), [1] PropReadcountWChildren (onecodex.lib.enums.Metric attribute), [1]

R

Rank (class in onecodex.lib.enums) Reaction (onecodex.lib.enums.FunctionalAnnotations attribute) Readcount (onecodex.lib.enums.Metric attribute), [1] ReadcountWChildren (onecodex.lib.enums.Metric attribute), [1] results() (onecodex.models.analysis.Alignments method) (onecodex.models.analysis.Analyses method) (onecodex.models.analysis.Classifications method) (onecodex.models.analysis.FunctionalProfiles method) (onecodex.models.analysis.Panels method)

results_key (onecodex.lib.enums.Metric property) Rpk (onecodex.lib.enums.FunctionalAnnotationsMetric attribute)

S

Samples (class in onecodex.models.sample) save() (onecodex.models.sample.Samples method) Shannon (onecodex.lib.enums.AlphaDiversityMetric attribute) Simpson (onecodex.lib.enums.AlphaDiversityMetric attribute)

Single (onecodex.lib.enums.Linkage attribute) Smacof (onecodex.lib.enums.OrdinationMethod attribute) Species (onecodex.lib.enums.Rank attribute) Superkingdom (onecodex.lib.enums.Rank attribute)

T

table() (onecodex.models.analysis.Classifications method) (onecodex.models.analysis.FunctionalProfiles method) Tags (class in onecodex.models.misc) to_classification_df() (onecodex.models.collection.SampleCollection method) to_df() (onecodex.models.collection.SampleCollection method)

to_functional_df() (onecodex.models.collection.SampleCollection method) to_otu() (onecodex.models.collection.SampleCollection method) tree_build() (onecodex.models.collection.SampleCollection method) tree_prune_rank() (onecodex.models.collection.SampleCollection method) tree_prune_tax_ids() (onecodex.models.collection.SampleCollection method)

U

unifrac() (onecodex.models.collection.SampleCollection method) UnweightedUnifrac (onecodex.lib.enums.BetaDiversityMetric attribute) upload() (onecodex.models.misc.Assets class method) (onecodex.models.misc.Documents class method) (onecodex.models.sample.Samples class method)

Users (class in onecodex.models.misc)

W

Weighted (onecodex.lib.enums.Linkage attribute) WeightedUnifrac (onecodex.lib.enums.BetaDiversityMetric attribute) where() (onecodex.models.analysis.Alignments class method) (onecodex.models.analysis.Analyses class method) (onecodex.models.analysis.Classifications class method) (onecodex.models.analysis.FunctionalProfiles class method) (onecodex.models.analysis.Panels class method) (onecodex.models.misc.Assets class method) (onecodex.models.misc.Documents class method) (onecodex.models.misc.Jobs class method) (onecodex.models.misc.Projects class method) (onecodex.models.misc.Tags class method) (onecodex.models.misc.Users class method) (onecodex.models.sample.Samples class method)