Flotilla
0.2.8dev
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flotilla
flotilla package
What’s new in the package
v0.2.8 (........)
v0.2.7 (April 20th, 2015)
v0.2.6 (April 10th, 2015)
v0.2.5 (March 3rd, 2015)
v0.2.4 (November 23rd, 2014)
v0.2.3 (November 17th, 2014)
v0.2.2 (November 7th, 2014)
v0.2.1 (November 6th, 2014)
v0.2.0 (November 5th, 2014)
OS X Installation instructions
Create a flotilla sandbox
Install and update all packages in your environment
Old OSX Installation instructions
Docker Instructions
API Reference
General use plots
Interactive plots
Machine learning plots
Splicing-specific plots
Create your very own datapackage!
Flotilla tutorial
Install flotilla
Create a datapackage
Computing on splicing data
Day to day helpful tips
Recreated papers
Page
Index
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
|
I
|
J
|
K
|
L
|
M
|
N
|
O
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P
|
R
|
S
|
T
|
U
|
V
|
W
|
X
|
Y
A
add_package_data_resource() (in module flotilla.util)
adjacency() (flotilla.compute.network.Networker method)
adjust_nums() (in module flotilla.external.combat)
apply_calc_robust() (in module flotilla.compute.generic)
apply_calc_rs() (in module flotilla.compute.generic)
apply_calc_slope() (in module flotilla.compute.generic)
apply_dcor() (in module flotilla.compute.generic)
aprior() (in module flotilla.external.combat)
as_numpy() (in module flotilla.util)
AssertionError
B
bar() (flotilla.visualize.splicing.ModalitiesViz method)
barplot() (in module flotilla.visualize.generic)
base_data() (in module flotilla.test.conftest)
BaseData (class in flotilla.data_model.base)
benjamini_hochberg() (in module flotilla.compute.expression)
big_nmf_space_transitions() (flotilla.data_model.base.BaseData method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.Study method)
(flotilla.data_model.study.Study method)
bin_range_strings() (in module flotilla.compute.infotheory)
binify() (flotilla.data_model.base.BaseData method)
(flotilla.ExpressionData method)
(flotilla.SplicingData method)
(flotilla.data_model.ExpressionData method)
(flotilla.data_model.SplicingData method)
(flotilla.data_model.expression.ExpressionData method)
(flotilla.data_model.splicing.SplicingData method)
(in module flotilla.compute.infotheory)
binify_and_jsd() (in module flotilla.compute.infotheory)
binned_nmf_reduced() (flotilla.data_model.base.BaseData method)
binned_reducer (flotilla.data_model.splicing.SplicingData attribute)
(flotilla.SplicingData attribute)
(flotilla.data_model.SplicingData attribute)
boolean_gene_categories() (in module flotilla.test.conftest)
bprior() (in module flotilla.external.combat)
builtin_predictor_configs (flotilla.compute.predict.PredictorConfigManager attribute)
(flotilla.PredictorConfigManager attribute)
C
cached_property (class in flotilla.util)
categorical (flotilla.compute.predict.Classifier attribute)
(flotilla.compute.predict.Regressor attribute)
celltype_event_counts (flotilla.data_model.Study attribute)
(flotilla.Study attribute)
,
[1]
(flotilla.data_model.study.Study attribute)
celltype_sizes() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.study.Study method)
check_a_feature() (flotilla.visualize.predict.ClassifierViz method)
check_if_already_downloaded() (in module flotilla.datapackage)
check_if_equal() (flotilla.compute.predict.PredictorDataSet method)
Classifier (class in flotilla.compute.predict)
ClassifierViz (class in flotilla.visualize.predict)
classify() (flotilla.data_model.base.BaseData method)
color_ordered() (in module flotilla.test.conftest)
colors (flotilla.visualize.splicing.ModalitiesViz attribute)
colors() (in module flotilla.test.conftest)
combat() (in module flotilla.external.combat)
ConfigOptimizer (class in flotilla.compute.predict)
cross_phenotype_jsd() (in module flotilla.compute.infotheory)
D
data_dir() (in module flotilla.test.conftest)
DataFrameICA (class in flotilla.compute.decomposition)
DataFrameNMF (class in flotilla.compute.decomposition)
DataFramePCA (class in flotilla.compute.decomposition)
DataFrameReducerBase (class in flotilla.compute.decomposition)
DataFrameTSNE (class in flotilla.compute.decomposition)
datapackage_url_to_dict() (in module flotilla.datapackage)
dataset (flotilla.compute.predict.PredictorBase attribute)
dataset() (flotilla.compute.predict.PredictorDataSetManager method)
(flotilla.PredictorDataSetManager method)
datasets (flotilla.compute.predict.PredictorDataSetManager attribute)
(flotilla.PredictorDataSetManager attribute)
DecompositionViz (class in flotilla.visualize.decomposition)
default_feature_set_ids (flotilla.data_model.Study attribute)
(flotilla.Study attribute)
,
[1]
(flotilla.data_model.study.Study attribute)
default_feature_subsets (flotilla.data_model.Study attribute)
(flotilla.Study attribute)
,
[1]
(flotilla.data_model.study.Study attribute)
default_predictor_scoring_fun() (in module flotilla.compute.predict)
default_sample_subsets (flotilla.data_model.Study attribute)
(flotilla.Study attribute)
,
[1]
(flotilla.data_model.study.Study attribute)
default_score_cutoff_fun() (in module flotilla.compute.predict)
design_mat() (in module flotilla.external.combat)
detect_outliers() (flotilla.data_model.base.BaseData method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.Study method)
(flotilla.data_model.study.Study method)
df_nonneg() (in module flotilla.test.conftest)
df_norm() (in module flotilla.test.conftest)
dict_to_str() (in module flotilla.util)
do_pca() (flotilla.visualize.predict.PredictorBaseViz method)
(flotilla.visualize.PredictorBaseViz method)
do_r() (in module flotilla.compute.generic)
domains (flotilla.data_model.gene_ontology.GeneOntologyData attribute)
(flotilla.GeneOntologyData attribute)
(flotilla.data_model.GeneOntologyData attribute)
draw_graph() (flotilla.visualize.network.NetworkerViz method)
draw_nonreduced_graph() (flotilla.visualize.network.NetworkerViz method)
drop_outliers() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.study.Study method)
dropna_mean() (in module flotilla.compute.generic)
E
enrichment() (flotilla.data_model.gene_ontology.GeneOntologyData method)
(flotilla.GeneOntologyData method)
(flotilla.data_model.GeneOntologyData method)
entropy() (in module flotilla.compute.infotheory)
event_estimation() (flotilla.visualize.splicing.ModalitiesViz method)
event_name() (in module flotilla.test.conftest)
events() (in module flotilla.test.conftest)
excluded_label (flotilla.data_model.splicing.SplicingData attribute)
(flotilla.SplicingData attribute)
(flotilla.data_model.SplicingData attribute)
expression_data() (in module flotilla.test.conftest)
expression_data_no_na() (in module flotilla.test.conftest)
expression_feature_data() (in module flotilla.test.conftest)
expression_feature_rename_col() (in module flotilla.test.conftest)
expression_kws() (in module flotilla.test.conftest)
expression_log_base() (in module flotilla.test.conftest)
expression_plus_one() (in module flotilla.test.conftest)
expression_thresh() (in module flotilla.test.conftest)
expression_vs_inconsistent_splicing() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.study.Study method)
ExpressionData (class in flotilla)
(class in flotilla.data_model)
(class in flotilla.data_model.expression)
F
feature_ids() (in module flotilla.test.conftest)
feature_renamer_series (flotilla.data_model.base.BaseData attribute)
feature_subset() (in module flotilla.test.conftest)
feature_subset_to_feature_ids() (flotilla.data_model.base.BaseData method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.Study method)
(flotilla.data_model.study.Study method)
feature_subsets (flotilla.data_model.base.BaseData attribute)
featurewise() (in module flotilla.test.conftest)
filter_splicing_on_expression() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.study.Study method)
fit() (flotilla.compute.decomposition.DataFrameNMF method)
(flotilla.compute.decomposition.DataFrameReducerBase method)
(flotilla.compute.predict.PredictorBase method)
fit_transform() (flotilla.compute.decomposition.DataFrameReducerBase method)
(flotilla.compute.decomposition.DataFrameTSNE method)
(flotilla.compute.splicing.ModalityEstimator method)
flotilla (module)
flotilla.compute (module)
flotilla.compute.decomposition (module)
flotilla.compute.expression (module)
flotilla.compute.generic (module)
flotilla.compute.infotheory (module)
flotilla.compute.network (module)
flotilla.compute.outlier (module)
flotilla.compute.predict (module)
flotilla.compute.splicing (module)
flotilla.data_model (module)
flotilla.data_model.base (module)
flotilla.data_model.expression (module)
flotilla.data_model.gene_ontology (module)
flotilla.data_model.metadata (module)
flotilla.data_model.quality_control (module)
flotilla.data_model.splicing (module)
flotilla.data_model.study (module)
flotilla.data_model.supplemental (module)
flotilla.datapackage (module)
flotilla.external (module)
flotilla.external.combat (module)
flotilla.test (module)
flotilla.test.conftest (module)
flotilla.test.test_embark (module)
flotilla.test.test_util (module)
flotilla.util (module)
flotilla.visualize (module)
flotilla.visualize.color (module)
flotilla.visualize.decomposition (module)
flotilla.visualize.expression (module)
flotilla.visualize.generic (module)
flotilla.visualize.ipython_interact (module)
flotilla.visualize.network (module)
flotilla.visualize.predict (module)
flotilla.visualize.splicing (module)
from_datapackage() (flotilla.data_model.Study class method)
(flotilla.Study class method)
,
[1]
(flotilla.data_model.study.Study class method)
from_datapackage_file() (flotilla.data_model.Study class method)
(flotilla.Study class method)
,
[1]
(flotilla.data_model.study.Study class method)
from_datapackage_url() (flotilla.data_model.Study class method)
(flotilla.Study class method)
,
[1]
(flotilla.data_model.study.Study class method)
G
gene_categories() (in module flotilla.test.conftest)
gene_name() (in module flotilla.test.conftest)
gene_ontology_data() (in module flotilla.test.conftest)
gene_ontology_data_path() (in module flotilla.test.conftest)
genelist_dropbox_link() (in module flotilla.test.conftest)
genelist_link() (in module flotilla.test.conftest)
genelist_path() (in module flotilla.test.conftest)
GeneOntologyData (class in flotilla)
(class in flotilla.data_model)
(class in flotilla.data_model.gene_ontology)
genes() (in module flotilla.test.conftest)
get_boosting_regressor() (in module flotilla.compute.generic)
get_dcor() (in module flotilla.compute.generic)
get_feature_subsets() (flotilla.visualize.Interactive static method)
(flotilla.visualize.ipython_interact.Interactive static method)
get_loading_method() (in module flotilla.util)
get_regressor() (in module flotilla.compute.generic)
get_robust_values() (in module flotilla.compute.generic)
get_slope() (in module flotilla.compute.generic)
get_switchy_score_order() (in module flotilla.compute.splicing)
get_unstarted_events() (in module flotilla.compute.generic)
get_weight_fun() (flotilla.compute.network.Networker method)
go_enrichment() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.study.Study method)
graph() (flotilla.compute.network.Networker method)
group_order() (in module flotilla.test.conftest)
group_to_color() (in module flotilla.test.conftest)
group_to_marker() (in module flotilla.test.conftest)
group_transitions() (in module flotilla.test.conftest)
groupby() (in module flotilla.test.conftest)
groups() (in module flotilla.test.conftest)
gstats() (flotilla.compute.expression.TwoWayGeneComparisonLocal method)
H
has_been_fit (flotilla.compute.predict.PredictorBase attribute)
has_been_scored (flotilla.compute.predict.PredictorBase attribute)
hist_single_vs_pooled_diff() (in module flotilla.visualize.splicing)
I
important_features_ (flotilla.compute.predict.PredictorBase attribute)
included_label (flotilla.data_model.splicing.SplicingData attribute)
(flotilla.SplicingData attribute)
(flotilla.data_model.SplicingData attribute)
initializers (flotilla.data_model.Study attribute)
(flotilla.Study attribute)
,
[1]
(flotilla.data_model.study.Study attribute)
install_development_package() (in module flotilla.util)
Interactive (class in flotilla.visualize)
(class in flotilla.visualize.ipython_interact)
interactive_choose_outliers() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
,
[2]
(flotilla.data_model.study.Study method)
(flotilla.visualize.Interactive static method)
(flotilla.visualize.ipython_interact.Interactive static method)
interactive_classifier() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
,
[2]
(flotilla.data_model.study.Study method)
(flotilla.visualize.Interactive static method)
(flotilla.visualize.ipython_interact.Interactive static method)
interactive_clustermap() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.study.Study method)
(flotilla.visualize.Interactive static method)
(flotilla.visualize.ipython_interact.Interactive static method)
interactive_correlations() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.study.Study method)
(flotilla.visualize.Interactive static method)
(flotilla.visualize.ipython_interact.Interactive static method)
interactive_graph() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
,
[2]
(flotilla.data_model.study.Study method)
(flotilla.visualize.Interactive static method)
(flotilla.visualize.ipython_interact.Interactive static method)
interactive_lavalamp_pooled_inconsistent() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
,
[2]
(flotilla.data_model.study.Study method)
(flotilla.visualize.Interactive static method)
(flotilla.visualize.ipython_interact.Interactive static method)
interactive_localZ() (flotilla.visualize.Interactive static method)
(flotilla.visualize.ipython_interact.Interactive static method)
interactive_pca() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
,
[2]
(flotilla.data_model.study.Study method)
(flotilla.visualize.Interactive static method)
(flotilla.visualize.ipython_interact.Interactive static method)
interactive_plot_modalities_lavalamps() (flotilla.visualize.Interactive static method)
(flotilla.visualize.ipython_interact.Interactive static method)
interactive_reset_outliers() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
,
[2]
(flotilla.data_model.study.Study method)
(flotilla.visualize.Interactive static method)
(flotilla.visualize.ipython_interact.Interactive static method)
it_sol() (in module flotilla.external.combat)
J
jsd() (in module flotilla.compute.infotheory)
jsd_2d() (flotilla.data_model.base.BaseData method)
jsd_df() (flotilla.data_model.base.BaseData method)
jsd_df_to_2d() (in module flotilla.compute.infotheory)
K
kld() (in module flotilla.compute.infotheory)
L
lavalamp() (in module flotilla.visualize.splicing)
lavalamp_pooled_inconsistent() (in module flotilla.visualize.splicing)
link_to_list() (in module flotilla.util)
load_csv() (in module flotilla.util)
load_gzip_pickle_df() (in module flotilla.util)
load_json() (in module flotilla.util)
load_pickle_df() (in module flotilla.util)
load_species_data() (flotilla.data_model.Study static method)
(flotilla.Study static method)
,
[1]
(flotilla.data_model.study.Study static method)
load_tsv() (in module flotilla.util)
logliks() (flotilla.compute.splicing.ModalityModel method)
logsumexp_logliks() (flotilla.compute.splicing.ModalityModel method)
M
make_study_datapackage() (in module flotilla)
(in module flotilla.datapackage)
mapping_stats_data() (in module flotilla.test.conftest)
mapping_stats_kws() (in module flotilla.test.conftest)
mapping_stats_min_reads_default() (in module flotilla.test.conftest)
mapping_stats_number_mapped_col() (in module flotilla.test.conftest)
MappingStatsData (class in flotilla)
(class in flotilla.data_model)
(class in flotilla.data_model.quality_control)
max_feature_scaler() (flotilla.compute.predict.PredictorConfigScalers static method)
maybe_make_directory() (flotilla.data_model.Study static method)
(flotilla.Study static method)
,
[1]
(flotilla.data_model.study.Study static method)
maybe_renamed_to_feature_id() (flotilla.data_model.base.BaseData method)
memoize() (in module flotilla.util)
MetaData (class in flotilla)
(class in flotilla.data_model)
(class in flotilla.data_model.metadata)
metadata_data() (in module flotilla.test.conftest)
metadata_kws() (in module flotilla.test.conftest)
metadata_minimum_samples() (in module flotilla.test.conftest)
ModalitiesViz (class in flotilla.visualize.splicing)
modality (flotilla.visualize.splicing.ModalitiesViz attribute)
modality_assignments() (flotilla.data_model.splicing.SplicingData method)
(flotilla.SplicingData method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.SplicingData method)
(flotilla.data_model.Study method)
(flotilla.data_model.study.Study method)
modality_colors (flotilla.visualize.splicing.ModalitiesViz attribute)
modality_counts() (flotilla.data_model.splicing.SplicingData method)
(flotilla.SplicingData method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.SplicingData method)
(flotilla.data_model.Study method)
(flotilla.data_model.study.Study method)
modality_models() (in module flotilla.test.conftest)
modality_order (flotilla.visualize.splicing.ModalitiesViz attribute)
ModalityEstimator (class in flotilla.compute.splicing)
ModalityModel (class in flotilla.compute.splicing)
N
n_components (flotilla.data_model.splicing.SplicingData attribute)
(flotilla.SplicingData attribute)
(flotilla.data_model.SplicingData attribute)
n_estimators_scaler() (flotilla.compute.predict.PredictorConfigScalers static method)
n_events() (in module flotilla.test.conftest)
n_genes() (in module flotilla.test.conftest)
n_good_features_ (flotilla.compute.predict.PredictorBase attribute)
n_groups() (in module flotilla.test.conftest)
n_jobs_scaler() (flotilla.compute.predict.PredictorConfigScalers static method)
n_phenotypes (flotilla.data_model.MetaData attribute)
(flotilla.MetaData attribute)
(flotilla.data_model.metadata.MetaData attribute)
n_samples() (in module flotilla.test.conftest)
na_thresh() (in module flotilla.test.conftest)
name_to_resource() (in module flotilla.datapackage)
natural_sort() (in module flotilla.util)
Networker (class in flotilla.compute.network)
NetworkerViz (class in flotilla.visualize.network)
new_dataset() (flotilla.compute.predict.PredictorDataSetManager method)
(flotilla.PredictorDataSetManager method)
new_predictor_config() (flotilla.compute.predict.PredictorConfigManager method)
(flotilla.PredictorConfigManager method)
nmf() (flotilla.compute.predict.PredictorBase method)
nmf_space_positions() (flotilla.data_model.base.BaseData method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.Study method)
(flotilla.data_model.study.Study method)
nmf_space_transitions() (flotilla.data_model.base.BaseData method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.Study method)
(flotilla.data_model.study.Study method)
(in module flotilla.visualize.generic)
number_mapped (flotilla.data_model.MappingStatsData attribute)
(flotilla.MappingStatsData attribute)
(flotilla.data_model.quality_control.MappingStatsData attribute)
O
objective_average_times_seen() (flotilla.compute.predict.ConfigOptimizer static method)
oob_score_ (flotilla.compute.predict.PredictorBase attribute)
OutlierDetection (class in flotilla.compute.outlier)
outliers (flotilla.data_model.base.BaseData attribute)
outliers() (in module flotilla.test.conftest)
P
parameters() (flotilla.compute.predict.PredictorConfig method)
pca() (flotilla.compute.predict.PredictorBase method)
percent_pooled_inconsistent() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.study.Study method)
percent_unique_celltype_events() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.study.Study method)
phenotype_col (flotilla.data_model.Study attribute)
(flotilla.Study attribute)
,
[1]
(flotilla.data_model.study.Study attribute)
phenotype_color_order (flotilla.data_model.MetaData attribute)
(flotilla.MetaData attribute)
(flotilla.data_model.metadata.MetaData attribute)
phenotype_color_ordered (flotilla.data_model.Study attribute)
(flotilla.Study attribute)
,
[1]
(flotilla.data_model.study.Study attribute)
phenotype_order (flotilla.data_model.MetaData attribute)
(flotilla.MetaData attribute)
(flotilla.Study attribute)
,
[1]
(flotilla.data_model.Study attribute)
(flotilla.data_model.metadata.MetaData attribute)
(flotilla.data_model.study.Study attribute)
phenotype_series (flotilla.data_model.MetaData attribute)
(flotilla.MetaData attribute)
(flotilla.data_model.metadata.MetaData attribute)
phenotype_to_color (flotilla.data_model.MetaData attribute)
(flotilla.MetaData attribute)
(flotilla.Study attribute)
,
[1]
(flotilla.data_model.Study attribute)
(flotilla.data_model.metadata.MetaData attribute)
(flotilla.data_model.study.Study attribute)
phenotype_to_marker (flotilla.data_model.MetaData attribute)
(flotilla.MetaData attribute)
(flotilla.Study attribute)
,
[1]
(flotilla.data_model.Study attribute)
(flotilla.data_model.metadata.MetaData attribute)
(flotilla.data_model.study.Study attribute)
phenotype_transitions (flotilla.data_model.MetaData attribute)
(flotilla.MetaData attribute)
(flotilla.Study attribute)
,
[1]
(flotilla.data_model.Study attribute)
(flotilla.data_model.metadata.MetaData attribute)
(flotilla.data_model.study.Study attribute)
plot() (flotilla.visualize.decomposition.DecompositionViz method)
(flotilla.visualize.PredictorBaseViz method)
(flotilla.visualize.expression.TwoWayScatterViz method)
(flotilla.visualize.predict.PredictorBaseViz method)
plot_big_nmf_space_transitions() (flotilla.data_model.base.BaseData method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.Study method)
(flotilla.data_model.study.Study method)
plot_classifier() (flotilla.data_model.base.BaseData method)
(flotilla.Study method)
,
[1]
,
[2]
(flotilla.data_model.Study method)
(flotilla.data_model.study.Study method)
plot_clustermap() (flotilla.data_model.base.BaseData method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.Study method)
(flotilla.data_model.study.Study method)
plot_correlations() (flotilla.data_model.base.BaseData method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.Study method)
(flotilla.data_model.study.Study method)
plot_dimensionality_reduction() (flotilla.data_model.base.BaseData method)
plot_event() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
,
[2]
(flotilla.data_model.study.Study method)
plot_event_modality_estimation() (flotilla.data_model.splicing.SplicingData method)
(flotilla.SplicingData method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.SplicingData method)
(flotilla.data_model.Study method)
(flotilla.data_model.study.Study method)
plot_explained_variance() (flotilla.visualize.decomposition.DecompositionViz method)
plot_expression_vs_inconsistent_splicing() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.study.Study method)
plot_feature() (flotilla.data_model.base.BaseData method)
(flotilla.SplicingData method)
(flotilla.data_model.SplicingData method)
(flotilla.data_model.splicing.SplicingData method)
plot_gene() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
,
[2]
(flotilla.data_model.study.Study method)
plot_graph() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
,
[2]
(flotilla.data_model.study.Study method)
plot_hist_single_vs_pooled_diff() (flotilla.data_model.splicing.SplicingData method)
(flotilla.SplicingData method)
(flotilla.data_model.SplicingData method)
plot_lavalamp() (flotilla.data_model.splicing.SplicingData method)
(flotilla.SplicingData method)
(flotilla.data_model.SplicingData method)
plot_lavalamp_pooled_inconsistent() (flotilla.data_model.splicing.SplicingData method)
(flotilla.SplicingData method)
(flotilla.Study method)
,
[1]
,
[2]
(flotilla.data_model.SplicingData method)
(flotilla.data_model.Study method)
(flotilla.data_model.study.Study method)
plot_lavalamps() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.study.Study method)
plot_loadings() (flotilla.visualize.decomposition.DecompositionViz method)
plot_loadings_heatmap() (flotilla.visualize.decomposition.DecompositionViz method)
plot_modalities_bars() (flotilla.data_model.splicing.SplicingData method)
(flotilla.SplicingData method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.SplicingData method)
(flotilla.data_model.Study method)
(flotilla.data_model.study.Study method)
plot_modalities_lavalamps() (flotilla.data_model.splicing.SplicingData method)
(flotilla.SplicingData method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.SplicingData method)
(flotilla.data_model.Study method)
(flotilla.data_model.study.Study method)
plot_modalities_reduced() (flotilla.data_model.splicing.SplicingData method)
(flotilla.SplicingData method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.SplicingData method)
(flotilla.data_model.Study method)
(flotilla.data_model.study.Study method)
plot_nmf_space_transitions() (flotilla.data_model.base.BaseData method)
plot_outliers() (flotilla.data_model.base.BaseData method)
plot_pca() (flotilla.data_model.base.BaseData method)
(flotilla.Study method)
,
[1]
,
[2]
(flotilla.data_model.Study method)
(flotilla.data_model.study.Study method)
plot_pooled_dot() (in module flotilla.visualize.generic)
plot_reduced_space() (flotilla.visualize.splicing.ModalitiesViz method)
plot_samples() (flotilla.visualize.decomposition.DecompositionViz method)
plot_scores() (flotilla.visualize.predict.PredictorBaseViz method)
(flotilla.visualize.PredictorBaseViz method)
plot_two_features() (flotilla.data_model.base.BaseData method)
(flotilla.SplicingData method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.SplicingData method)
(flotilla.data_model.Study method)
(flotilla.data_model.splicing.SplicingData method)
(flotilla.data_model.study.Study method)
plot_two_samples() (flotilla.data_model.base.BaseData method)
(flotilla.SplicingData method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.SplicingData method)
(flotilla.data_model.Study method)
(flotilla.data_model.splicing.SplicingData method)
(flotilla.data_model.study.Study method)
plot_violins() (flotilla.visualize.decomposition.DecompositionViz method)
pooled (flotilla.data_model.base.BaseData attribute)
pooled() (in module flotilla.test.conftest)
pooled_inconsistent() (flotilla.data_model.splicing.SplicingData method)
(flotilla.SplicingData method)
(flotilla.data_model.SplicingData method)
postmean() (in module flotilla.external.combat)
postvar() (in module flotilla.external.combat)
predict() (flotilla.compute.outlier.OutlierDetection method)
(flotilla.compute.predict.PredictorBase method)
predictor (flotilla.compute.predict.PredictorBase attribute)
predictor() (flotilla.compute.predict.PredictorDataSet method)
predictor_config() (flotilla.compute.predict.PredictorConfigManager method)
(flotilla.PredictorConfigManager method)
predictor_configs (flotilla.compute.predict.PredictorConfigManager attribute)
(flotilla.PredictorConfigManager attribute)
PredictorBase (class in flotilla.compute.predict)
PredictorBaseViz (class in flotilla.visualize)
(class in flotilla.visualize.predict)
PredictorConfig (class in flotilla.compute.predict)
PredictorConfigManager (class in flotilla)
(class in flotilla.compute.predict)
PredictorConfigScalers (class in flotilla.compute.predict)
PredictorDataSet (class in flotilla.compute.predict)
PredictorDataSetManager (class in flotilla)
(class in flotilla.compute.predict)
predictors (flotilla.compute.predict.PredictorDataSet attribute)
R
RANDOM_STATE() (in module flotilla.test.conftest)
raw_reducer (flotilla.data_model.splicing.SplicingData attribute)
(flotilla.SplicingData attribute)
(flotilla.data_model.SplicingData attribute)
readers (flotilla.data_model.Study attribute)
(flotilla.Study attribute)
,
[1]
(flotilla.data_model.study.Study attribute)
reduce() (flotilla.data_model.base.BaseData method)
Regressor (class in flotilla.compute.predict)
RegressorViz (class in flotilla.visualize.predict)
relabel_pcs() (flotilla.compute.decomposition.DataFrameReducerBase static method)
renamed() (in module flotilla.test.conftest)
S
sample_id_to_color (flotilla.data_model.MetaData attribute)
(flotilla.MetaData attribute)
(flotilla.Study attribute)
,
[1]
(flotilla.data_model.Study attribute)
(flotilla.data_model.metadata.MetaData attribute)
(flotilla.data_model.study.Study attribute)
sample_id_to_phenotype (flotilla.data_model.MetaData attribute)
(flotilla.MetaData attribute)
(flotilla.Study attribute)
,
[1]
(flotilla.data_model.Study attribute)
(flotilla.data_model.metadata.MetaData attribute)
(flotilla.data_model.study.Study attribute)
sample_ids() (in module flotilla.test.conftest)
sample_subset() (in module flotilla.test.conftest)
sample_subset_to_sample_ids() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.study.Study method)
sample_subsets (flotilla.data_model.MetaData attribute)
(flotilla.MetaData attribute)
(flotilla.data_model.metadata.MetaData attribute)
samples() (in module flotilla.test.conftest)
save() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.study.Study method)
score_coefficient (flotilla.compute.predict.PredictorBase attribute)
score_cutoff_ (flotilla.compute.predict.PredictorBase attribute)
scores_ (flotilla.compute.predict.PredictorBase attribute)
serve_ipython() (in module flotilla.util)
set_reducer_plotting_args() (flotilla.visualize.predict.PredictorBaseViz method)
(flotilla.visualize.PredictorBaseViz method)
shorten() (flotilla.visualize.decomposition.DecompositionViz method)
simple_twoway_scatter() (in module flotilla.visualize.generic)
singles (flotilla.data_model.base.BaseData attribute)
spearmanr_dataframe() (in module flotilla.compute.generic)
spearmanr_series() (in module flotilla.compute.generic)
SpikeInData (class in flotilla)
(class in flotilla.data_model)
(class in flotilla.data_model.expression)
splicing() (in module flotilla.test.conftest)
splicing_data() (in module flotilla.test.conftest)
splicing_feature_common_id() (in module flotilla.test.conftest)
splicing_feature_data() (in module flotilla.test.conftest)
splicing_kws() (in module flotilla.test.conftest)
SplicingData (class in flotilla)
(class in flotilla.data_model)
(class in flotilla.data_model.splicing)
standardize() (in module flotilla.test.conftest)
Study (class in flotilla)
,
[1]
(class in flotilla.data_model)
(class in flotilla.data_model.study)
subset_ (flotilla.compute.predict.PredictorBase attribute)
subsets_from_metadata() (in module flotilla.data_model.base)
SupplementalData (class in flotilla.data_model.supplemental)
switchy_score() (in module flotilla.compute.splicing)
T
technical_outliers() (in module flotilla.test.conftest)
test_embark() (in module flotilla.test.test_embark)
test_link_to_list() (in module flotilla.test.test_util)
timeout() (in module flotilla.util)
TimeoutError
timestamp() (in module flotilla.util)
to_base_file_tuple() (in module flotilla.util)
too_few_mapped (flotilla.data_model.MappingStatsData attribute)
(flotilla.MappingStatsData attribute)
(flotilla.data_model.quality_control.MappingStatsData attribute)
traitset (flotilla.compute.predict.PredictorDataSet attribute)
transform() (flotilla.compute.decomposition.DataFrameReducerBase method)
transition_distances() (flotilla.data_model.base.BaseData static method)
true_modalities() (in module flotilla.test.conftest)
TwoWayGeneComparisonLocal (class in flotilla.compute.expression)
TwoWayScatterViz (class in flotilla.visualize.expression)
U
unique_celltype_event_counts() (flotilla.data_model.Study method)
(flotilla.Study method)
,
[1]
(flotilla.data_model.study.Study method)
unique_phenotypes (flotilla.data_model.MetaData attribute)
(flotilla.MetaData attribute)
(flotilla.data_model.metadata.MetaData attribute)
V
validate_params() (in module flotilla.util)
variant (flotilla.data_model.base.BaseData attribute)
violinplot() (in module flotilla.visualize.generic)
W
weight_funs (flotilla.compute.network.Networker attribute)
write_csv() (in module flotilla.util)
write_gzip_pickle_df() (in module flotilla.util)
write_pickle_df() (in module flotilla.util)
write_tsv() (in module flotilla.util)
X
X (flotilla.compute.predict.PredictorBase attribute)
(flotilla.compute.predict.PredictorDataSet attribute)
x_norm() (in module flotilla.test.conftest)
Y
y (flotilla.compute.predict.PredictorBase attribute)
(flotilla.compute.predict.PredictorDataSet attribute)
Olga B. Botvinnik
is funded by the
NDSEG
fellowship and is a
NumFOCUS
John Hunter Technology Fellow
.
Michael T. Lovci was partially funded by a fellowship from
Genentech
. Partially funded by
NIH
grants NS075449 and HG004659 and
CIRM
grants RB4-06045 and TR3-05676 to
Gene Yeo
.