calour docs
2018.10.1
Site
General Calour concepts
Microbiome tutorials
Metabolome tutorials
Using Calour functions via the module and the Experiment class
Main classes and utility functions
Functions operating on
Experiment
object
Creating database interfaces for Calour
Page
Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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L
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N
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P
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R
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S
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T
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U
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__deepcopy__() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
__eq__() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
__getitem__() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
__ne__() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
__repr__() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(calour.training.SortedStratifiedKFold method)
A
add_sample_metadata_as_features() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.training)
add_terms_to_features() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.database)
aggregate_by_metadata() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.manipulation)
AmpliconExperiment (class in calour.amplicon_experiment)
B
binarize() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.transforming)
C
calour.amplicon_experiment (module)
calour.analysis (module)
calour.database (module)
calour.experiment (module)
calour.export_html (module)
calour.filtering (module)
calour.heatmap (module)
calour.io (module)
calour.manipulation (module)
calour.plotting (module)
calour.sorting (module)
calour.training (module)
calour.transforming (module)
calour.util (module)
center_log_ratio() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.transforming)
classify() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.training)
cluster_data() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.sorting)
cluster_features() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.sorting)
collapse_taxonomy() (calour.amplicon_experiment.AmpliconExperiment method)
compute_prevalence() (in module calour.util)
copy() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
correlation() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.analysis)
D
diff_abundance() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.analysis)
diff_abundance_kw() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.analysis)
downsample() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.filtering)
E
enrichment() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.database)
Experiment (class in calour.experiment)
export_html() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.export_html)
F
filter_abundance() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.filtering)
filter_by_data() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.filtering)
filter_by_metadata() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.filtering)
filter_fasta() (calour.amplicon_experiment.AmpliconExperiment method)
filter_ids() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.filtering)
filter_mean_abundance() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.filtering)
filter_orig_reads() (calour.amplicon_experiment.AmpliconExperiment method)
filter_prevalence() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.filtering)
filter_sample_categories() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.filtering)
filter_samples() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.filtering)
filter_samples_() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
filter_taxonomy() (calour.amplicon_experiment.AmpliconExperiment method)
find_lowest_taxonomy() (calour.amplicon_experiment.AmpliconExperiment method)
freq_ratio() (in module calour.filtering)
from_pandas() (calour.amplicon_experiment.AmpliconExperiment class method)
(calour.experiment.Experiment class method)
G
get_data() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
get_n_splits() (calour.training.RepeatedSortedStratifiedKFold method)
(calour.training.SortedStratifiedKFold method)
H
heatmap() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.heatmap)
I
is_abundant() (in module calour.filtering)
is_prevalent() (in module calour.filtering)
J
join_experiments() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.manipulation)
join_experiments_featurewise() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
join_metadata_fields() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.manipulation)
L
learning_curve_depths() (calour.amplicon_experiment.AmpliconExperiment method)
log_n() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.transforming)
N
normalize() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.transforming)
normalize_by_subset_features() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.transforming)
normalize_compositional() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.transforming)
P
plot() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.heatmap)
plot_abund_prevalence() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.plotting)
plot_cm() (in module calour.training)
plot_core_features() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.plotting)
plot_diff_abundance_enrichment() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.plotting)
plot_enrichment() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.plotting)
plot_feature_matrix() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.plotting)
plot_hist() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.plotting)
plot_prc() (in module calour.training)
plot_roc() (in module calour.training)
plot_scatter() (in module calour.training)
plot_stacked_bar() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.plotting)
R
random_permute_data() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.transforming)
read() (in module calour.io)
read_amplicon() (in module calour.io)
read_ms() (in module calour.io)
register_functions() (in module calour.util)
regress() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.training)
reorder() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
RepeatedSortedStratifiedKFold (class in calour.training)
rescale() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
S
save() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.io)
save_biom() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.io)
save_fasta() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
save_metadata() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.io)
scale() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.transforming)
set_log_level() (in module calour.util)
shape (calour.amplicon_experiment.AmpliconExperiment attribute)
(calour.experiment.Experiment attribute)
sort_abundance() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.sorting)
sort_by_data() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.sorting)
sort_by_metadata() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.sorting)
sort_centroid() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.sorting)
sort_ids() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.sorting)
sort_samples() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.sorting)
sort_taxonomy() (calour.amplicon_experiment.AmpliconExperiment method)
SortedStratifiedKFold (class in calour.training)
sparse (calour.amplicon_experiment.AmpliconExperiment attribute)
(calour.experiment.Experiment attribute)
split() (calour.training.RepeatedSortedStratifiedKFold method)
(calour.training.SortedStratifiedKFold method)
split_taxonomy() (calour.amplicon_experiment.AmpliconExperiment method)
split_train_test() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
subsample_count() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.transforming)
T
to_pandas() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
transform() (calour.amplicon_experiment.AmpliconExperiment method)
(calour.experiment.Experiment method)
(in module calour.transforming)
U
unique_cut() (in module calour.filtering)
