Microbial Co-occurrence Network Explorer
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Example pipeline setup and execution
Data Import and Export (Python API)
micone
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Microbial Co-occurrence Network Explorer
Index
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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
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I
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J
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
A
abundance (micone.validation.network_schema.NodeModel attribute)
authors (micone.validation.network_schema.PublicationModel attribute)
B
BaseLineage (in module micone.main.lineage)
BiomType (class in micone.validation.otu_schema)
C
children (micone.validation.network_schema.NodeModel attribute)
ChildrenmapType (class in micone.validation.network_schema)
Class (micone.main.lineage.Lineage attribute)
cleanup() (micone.logging.logger.Log method)
cmd (micone.pipelines.command.Command property)
collapse_taxa() (micone.main.otu.Otu method)
combine_pvalues() (micone.main.network_group.NetworkGroup method)
Command (class in micone.pipelines.command)
computational_metadata (micone.validation.network_schema.NetworkmetadataModel attribute)
condition (micone.validation.network_schema.MetadataModel attribute)
(micone.validation.network_schema.NetworkmetadataModel attribute)
config (micone.logging.logger.Log attribute)
configs (micone.setup.environments.Environments attribute)
configuration (micone.validation.otu_validator.OtuValidator property)
contexts (micone.main.network_group.NetworkGroup property)
CorrelationmatrixType (class in micone.validation.network_schema)
D
DataType (class in micone.validation.otu_schema)
date (micone.validation.network_schema.PublicationModel attribute)
default_to_qiime2() (in module micone.conversion.taxmetadata_converter)
description (micone.validation.network_schema.MetadataModel attribute)
(micone.validation.network_schema.NetworkmetadataModel attribute)
directionality (micone.validation.network_schema.NetworkmetadataModel attribute)
E
ElistType (class in micone.validation.network_schema)
enable() (micone.logging.logger.Log method)
env_names (micone.setup.environments.Environments attribute)
Environments (class in micone.setup.environments)
error (micone.pipelines.command.Command property)
experimental_metadata (micone.validation.network_schema.MetadataModel attribute)
(micone.validation.network_schema.NetworkmetadataModel attribute)
F
fail() (micone.utils.spinner.Spinner method)
Family (micone.main.lineage.Lineage attribute)
filter() (micone.main.network.Network method)
(micone.main.network_group.NetworkGroup method)
(micone.main.otu.Otu method)
from_str() (micone.main.lineage.Lineage class method)
from_taxid() (micone.main.lineage.Lineage class method)
G
Genus (micone.main.lineage.Lineage attribute)
get_adjacency_table() (micone.main.network.Network method)
get_adjacency_vectors() (micone.main.network_group.NetworkGroup method)
get_consensus_network() (micone.main.network_group.NetworkGroup method)
get_superset() (micone.main.lineage.Lineage method)
graph (micone.main.network.Network attribute)
(micone.main.network_group.NetworkGroup attribute)
H
HeaderType (class in micone.validation.otu_schema)
host (micone.validation.network_schema.MetadataModel attribute)
(micone.validation.network_schema.NetworkmetadataModel attribute)
I
id (micone.validation.network_schema.NodeModel attribute)
IndexType (class in micone.validation.otu_schema)
init() (micone.setup.environments.Environments method)
interaction_type (micone.validation.network_schema.NetworkmetadataModel attribute)
InteractionmatrixType (class in micone.validation.network_schema)
interactive (micone.utils.spinner.Spinner attribute)
is_norm() (micone.main.otu.Otu method)
J
json() (micone.main.network.Network method)
(micone.main.network_group.NetworkGroup method)
json_to_elist() (in module micone.conversion.network_converter)
K
Kingdom (micone.main.lineage.Lineage attribute)
L
Lineage (class in micone.main.lineage)
lineage (micone.validation.network_schema.NodeModel attribute)
LinkModel (class in micone.validation.network_schema)
links (micone.main.network.Network property)
(micone.main.network_group.NetworkGroup property)
(micone.validation.network_schema.LinksModel attribute)
LinksModel (class in micone.validation.network_schema)
load() (micone.setup.environments.Environments method)
load_data() (micone.main.network.Network class method)
(micone.main.otu.Otu class method)
load_elist() (micone.main.network.Network class method)
load_graph() (micone.main.network.Network class method)
load_json() (micone.main.network.Network class method)
(micone.main.network_group.NetworkGroup class method)
load_validate() (micone.validation.otu_validator.OtuValidator method)
location (micone.validation.network_schema.MetadataModel attribute)
(micone.validation.network_schema.NetworkmetadataModel attribute)
Log (class in micone.logging.logger)
log() (micone.pipelines.command.Command method)
logger (micone.logging.logger.Log attribute)
M
main() (in module micone.cli)
MESSAGES (micone.validation.network_schema.ChildrenmapType attribute)
(micone.validation.network_schema.CorrelationmatrixType attribute)
(micone.validation.network_schema.ElistType attribute)
(micone.validation.network_schema.InteractionmatrixType attribute)
(micone.validation.network_schema.PvaluematrixType attribute)
(micone.validation.otu_schema.BiomType attribute)
(micone.validation.otu_schema.DataType attribute)
(micone.validation.otu_schema.HeaderType attribute)
(micone.validation.otu_schema.IndexType attribute)
(micone.validation.otu_schema.ObsmetaType attribute)
(micone.validation.otu_schema.SamplemetaType attribute)
metadata (micone.main.network.Network property)
MetadataModel (class in micone.validation.network_schema)
micone
module
micone.cli
module
micone.conversion
module
micone.conversion.network_converter
module
micone.conversion.otu_converter
module
micone.conversion.taxmetadata_converter
module
micone.logging
module
micone.logging.logger
module
micone.main
module
micone.main.lineage
module
micone.main.network
module
micone.main.network_group
module
micone.main.otu
module
micone.micone
module
micone.pipelines
module
micone.pipelines.command
module
micone.setup
module
micone.setup.environments
module
micone.utils
module
micone.utils.spinner
module
micone.validation
module
micone.validation.network_schema
module
micone.validation.otu_schema
module
micone.validation.otu_validator
module
module
micone
micone.cli
micone.conversion
micone.conversion.network_converter
micone.conversion.otu_converter
micone.conversion.taxmetadata_converter
micone.logging
micone.logging.logger
micone.main
micone.main.lineage
micone.main.network
micone.main.network_group
micone.main.otu
micone.micone
micone.pipelines
micone.pipelines.command
micone.setup
micone.setup.environments
micone.utils
micone.utils.spinner
micone.validation
micone.validation.network_schema
micone.validation.otu_schema
micone.validation.otu_validator
N
name (micone.main.lineage.Lineage property)
(micone.validation.network_schema.NodeModel attribute)
Network (class in micone.main.network)
NetworkGroup (class in micone.main.network_group)
NetworkmetadataModel (class in micone.validation.network_schema)
NodeModel (class in micone.validation.network_schema)
nodes (micone.main.network.Network property)
(micone.main.network_group.NetworkGroup property)
(micone.validation.network_schema.NodesModel attribute)
NodesModel (class in micone.validation.network_schema)
normalize() (micone.main.otu.Otu method)
O
obs_metadata (micone.main.otu.Otu property)
ObsmetaType (class in micone.validation.otu_schema)
Order (micone.main.lineage.Lineage attribute)
Otu (class in micone.main.otu)
otu_data (micone.main.otu.Otu attribute)
OtuValidator (class in micone.validation.otu_validator)
output (micone.pipelines.command.Command property)
P
partition() (micone.main.otu.Otu method)
path (micone.logging.logger.Log attribute)
pcorr_methods (micone.main.network.Network property)
Phylum (micone.main.lineage.Lineage attribute)
post_install() (micone.setup.environments.Environments method)
proc_cmd_sync() (micone.pipelines.command.Command method)
process (micone.pipelines.command.Command attribute)
profile (micone.pipelines.command.Command attribute)
project (micone.pipelines.command.Command attribute)
publication (micone.validation.network_schema.MetadataModel attribute)
(micone.validation.network_schema.NetworkmetadataModel attribute)
PublicationModel (class in micone.validation.network_schema)
pubmed_id (micone.validation.network_schema.PublicationModel attribute)
pvalue (micone.validation.network_schema.LinkModel attribute)
PvaluematrixType (class in micone.validation.network_schema)
Q
qiime1_to_default() (in module micone.conversion.taxmetadata_converter)
qiime2_to_default() (in module micone.conversion.taxmetadata_converter)
R
rm_sparse_obs() (micone.main.otu.Otu method)
rm_sparse_samples() (micone.main.otu.Otu method)
run() (micone.pipelines.command.Command method)
S
sample_metadata (micone.main.otu.Otu property)
SamplemetaType (class in micone.validation.otu_schema)
source (micone.validation.network_schema.LinkModel attribute)
Species (micone.main.lineage.Lineage attribute)
Spinner (class in micone.utils.spinner)
start() (micone.utils.spinner.Spinner method)
status (micone.pipelines.command.Command property)
stop() (micone.utils.spinner.Spinner method)
succeed() (micone.utils.spinner.Spinner method)
T
target (micone.validation.network_schema.LinkModel attribute)
tax_level (micone.main.otu.Otu property)
taxid (micone.main.lineage.Lineage property)
(micone.validation.network_schema.NodeModel attribute)
taxlevel (micone.validation.network_schema.NodeModel attribute)
text (micone.utils.spinner.Spinner property)
to_dict() (micone.main.lineage.Lineage method)
to_network() (micone.main.network_group.NetworkGroup method)
to_str() (micone.main.lineage.Lineage method)
U
update() (micone.pipelines.command.Command method)
update_thresholds() (micone.main.network_group.NetworkGroup method)
V
validate_data() (micone.validation.network_schema.InteractionmatrixType method)
(micone.validation.otu_schema.BiomType method)
validate_data_npfloat() (micone.validation.otu_schema.DataType method)
validate_data_range() (micone.validation.network_schema.CorrelationmatrixType method)
(micone.validation.network_schema.PvaluematrixType method)
(micone.validation.otu_schema.DataType method)
validate_header() (micone.validation.otu_schema.HeaderType method)
validate_headers() (micone.validation.network_schema.InteractionmatrixType method)
validate_headers_index() (micone.validation.network_schema.ElistType method)
validate_index() (micone.validation.otu_schema.BiomType method)
(micone.validation.otu_schema.ObsmetaType method)
validate_index_str() (micone.validation.otu_schema.IndexType method)
validate_index_unique() (micone.validation.otu_schema.IndexType method)
validate_isdataframe() (micone.validation.network_schema.InteractionmatrixType method)
validate_istable() (micone.validation.otu_schema.BiomType method)
validate_keys() (micone.validation.network_schema.ChildrenmapType method)
validate_obs_metadata() (micone.validation.otu_schema.BiomType method)
validate_obsmeta_data() (micone.validation.otu_schema.ObsmetaType method)
validate_obsmeta_headers() (micone.validation.otu_schema.ObsmetaType method)
validate_sample_metadata() (micone.validation.otu_schema.BiomType method)
validate_samplemeta_columns() (micone.validation.otu_schema.SamplemetaType method)
validate_samplemeta_index() (micone.validation.otu_schema.SamplemetaType method)
validate_samples() (micone.validation.otu_schema.BiomType method)
validate_structure() (micone.validation.otu_schema.SamplemetaType method)
validate_symmetry() (micone.validation.network_schema.InteractionmatrixType method)
validate_values() (micone.validation.network_schema.ChildrenmapType method)
validator (micone.validation.otu_validator.OtuValidator attribute)
W
wait() (micone.pipelines.command.Command method)
weight (micone.validation.network_schema.LinkModel attribute)
write() (micone.main.network.Network method)
(micone.main.network_group.NetworkGroup method)
(micone.main.otu.Otu method)
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