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) all() (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.Mlsts class method) (onecodex.models.analysis.Panels class method) (onecodex.models.analysis.Workflows class method) (onecodex.models.base.OneCodexBase 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.Metadata class method) (onecodex.models.sample.Samples class method)

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) await_completion() (onecodex.models.analysis.Alignments method) (onecodex.models.analysis.Analyses method) (onecodex.models.analysis.Classifications method) (onecodex.models.analysis.FunctionalProfiles method) (onecodex.models.analysis.Mlsts method) (onecodex.models.analysis.Panels method) (onecodex.models.analysis.Workflows method)

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

cancel() (onecodex.models.analysis.Alignments method) (onecodex.models.analysis.Analyses method) (onecodex.models.analysis.Classifications method) (onecodex.models.analysis.FunctionalProfiles method) (onecodex.models.analysis.Mlsts method) (onecodex.models.analysis.Panels method) (onecodex.models.analysis.Workflows method) 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)

create() (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.Mlsts class method) (onecodex.models.analysis.Panels class method) (onecodex.models.analysis.Workflows class method) (onecodex.models.base.OneCodexBase 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.Metadata class method) (onecodex.models.sample.Samples class method)

D

delete() (onecodex.models.analysis.Alignments method) (onecodex.models.analysis.Analyses method) (onecodex.models.analysis.Classifications method) (onecodex.models.analysis.FunctionalProfiles method) (onecodex.models.analysis.Mlsts method) (onecodex.models.analysis.Panels method) (onecodex.models.analysis.Workflows method) (onecodex.models.base.OneCodexBase method) (onecodex.models.misc.Assets method) (onecodex.models.misc.Documents method) (onecodex.models.misc.Jobs method) (onecodex.models.misc.Projects method) (onecodex.models.misc.Tags method) (onecodex.models.misc.Users method) (onecodex.models.sample.Metadata method) (onecodex.models.sample.Samples method)

details() (onecodex.models.misc.Jobs method) 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.Mlsts method) (onecodex.models.analysis.Panels method) (onecodex.models.analysis.Workflows 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) FilteredReadcount (onecodex.lib.enums.Metric attribute), [1]

FilteredReadcountWChildren (onecodex.lib.enums.Metric attribute), [1] 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() (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.Mlsts class method) (onecodex.models.analysis.Panels class method) (onecodex.models.analysis.Workflows class method) (onecodex.models.base.OneCodexBase 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.Metadata class method) (onecodex.models.sample.Samples class method)

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.Mlsts method) (onecodex.models.analysis.Panels method) (onecodex.models.analysis.Workflows method) Go (onecodex.lib.enums.FunctionalAnnotations attribute)

I

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

is_abundance_sensitive (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) logs() (onecodex.models.analysis.Alignments method) (onecodex.models.analysis.Analyses method) (onecodex.models.analysis.Classifications method) (onecodex.models.analysis.FunctionalProfiles method) (onecodex.models.analysis.Mlsts method) (onecodex.models.analysis.Panels method) (onecodex.models.analysis.Workflows method)

M

Manhattan (onecodex.lib.enums.BetaDiversityMetric attribute) Median (onecodex.lib.enums.Linkage attribute) MetaCyc (onecodex.lib.enums.FunctionalAnnotations attribute) Metadata (class in onecodex.models.sample) Metric (class in onecodex.lib.enums) Mlsts (class in onecodex.models.analysis) 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.Mlsts attribute) (onecodex.models.analysis.Panels attribute) (onecodex.models.analysis.Workflows attribute) (onecodex.models.base.OneCodexBase 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.Metadata attribute) (onecodex.models.sample.Samples attribute)

N

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

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

O

ObservedTaxa (onecodex.lib.enums.AlphaDiversityMetric attribute) OneCodexBase (class in onecodex.models.base)

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] refresh() (onecodex.models.analysis.Alignments method) (onecodex.models.analysis.Analyses method) (onecodex.models.analysis.Classifications method) (onecodex.models.analysis.FunctionalProfiles method) (onecodex.models.analysis.Mlsts method) (onecodex.models.analysis.Panels method) (onecodex.models.analysis.Workflows method)

results() (onecodex.models.analysis.Alignments method) (onecodex.models.analysis.Analyses method) (onecodex.models.analysis.Classifications method) (onecodex.models.analysis.FunctionalProfiles method) (onecodex.models.analysis.Mlsts method) (onecodex.models.analysis.Panels method) (onecodex.models.analysis.Workflows method) results_key (onecodex.lib.enums.Metric property) Rpk (onecodex.lib.enums.FunctionalAnnotationsMetric attribute)

S

Samples (class in onecodex.models.sample) save() (onecodex.models.analysis.Alignments method) (onecodex.models.analysis.Analyses method) (onecodex.models.analysis.Classifications method) (onecodex.models.analysis.FunctionalProfiles method) (onecodex.models.analysis.Mlsts method) (onecodex.models.analysis.Panels method) (onecodex.models.analysis.Workflows method) (onecodex.models.base.OneCodexBase method) (onecodex.models.misc.Assets method) (onecodex.models.misc.Documents method) (onecodex.models.misc.Jobs method) (onecodex.models.misc.Projects method) (onecodex.models.misc.Tags method) (onecodex.models.misc.Users method) (onecodex.models.sample.Metadata method) (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) update() (onecodex.models.analysis.Alignments method) (onecodex.models.analysis.Analyses method) (onecodex.models.analysis.Classifications method) (onecodex.models.analysis.FunctionalProfiles method) (onecodex.models.analysis.Mlsts method) (onecodex.models.analysis.Panels method) (onecodex.models.analysis.Workflows method) (onecodex.models.base.OneCodexBase method) (onecodex.models.misc.Assets method) (onecodex.models.misc.Documents method) (onecodex.models.misc.Jobs method) (onecodex.models.misc.Projects method) (onecodex.models.misc.Tags method) (onecodex.models.misc.Users method) (onecodex.models.sample.Metadata method) (onecodex.models.sample.Samples method)

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.Mlsts class method) (onecodex.models.analysis.Panels class method) (onecodex.models.analysis.Workflows class method) (onecodex.models.base.OneCodexBase 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.Metadata class method) (onecodex.models.sample.Samples class method)

Workflows (class in onecodex.models.analysis)