metage2metabo
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Requirements and Installation
Commands
m2m Inputs
m2m Tutorial
m2m Outputs
Supplementary information
m2m’s API
m2m_analysis
Troubleshooting
metage2metabo
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Index
A
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B
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C
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E
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F
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G
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I
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M
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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
A
add_targets_to_instance() (in module metage2metabo.m2m.m2m_workflow)
addedvalue() (in module metage2metabo.m2m.community_addedvalue)
analyze_indiv_scope() (in module metage2metabo.m2m.individual_scope)
analyze_recon() (in module metage2metabo.m2m.reconstruction)
B
bbl_to_html() (in module metage2metabo.m2m_analysis.graph_compression)
bbl_to_svg() (in module metage2metabo.m2m_analysis.graph_compression)
C
check_absolute_path() (in module metage2metabo.utils)
check_oog_jar_file() (in module metage2metabo.m2m_analysis.graph_compression)
check_program() (in module metage2metabo.utils)
comm_scope_run() (in module metage2metabo.m2m.community_scope)
compare_seeds_and_targets() (in module metage2metabo.sbml_management)
compression() (in module metage2metabo.m2m_analysis.graph_compression)
compute_mincom() (in module metage2metabo.m2m.minimal_community)
convert_groups_to_equation() (in module metage2metabo.m2m_analysis.enumeration)
convert_taxon_id() (in module metage2metabo.m2m_analysis.graph_compression)
create_gml() (in module metage2metabo.m2m_analysis.solution_graph)
create_metadata() (in module metage2metabo.__main__)
create_padmet_stat() (in module metage2metabo.m2m.reconstruction)
create_sbml_stat() (in module metage2metabo.m2m.reconstruction)
create_species_sbml() (in module metage2metabo.sbml_management)
cscope() (in module metage2metabo.m2m.community_scope)
E
enumeration() (in module metage2metabo.m2m_analysis.enumeration)
enumeration_analysis() (in module metage2metabo.m2m_analysis.enumeration)
extract_groups_from_enumeration() (in module metage2metabo.m2m_analysis.enumeration)
extract_taxa() (in module metage2metabo.m2m_analysis.taxonomy)
F
file_or_folder() (in module metage2metabo.utils)
G
genomes_to_pgdb() (in module metage2metabo.m2m.reconstruction)
get_basename() (in module metage2metabo.utils)
get_compounds() (in module metage2metabo.sbml_management)
get_extension() (in module metage2metabo.utils)
get_taxon() (in module metage2metabo.m2m_analysis.taxonomy)
graph_analysis() (in module metage2metabo.m2m_analysis.solution_graph)
I
indiv_scope_on_species() (in module metage2metabo.m2m.individual_scope)
indiv_scope_run() (in module metage2metabo.m2m.individual_scope)
instance_community() (in module metage2metabo.m2m.community_scope)
is_valid_dir() (in module metage2metabo.utils)
is_valid_file() (in module metage2metabo.utils)
is_valid_path() (in module metage2metabo.utils)
iscope() (in module metage2metabo.m2m.individual_scope)
M
main() (in module metage2metabo.__main__)
main_added_value() (in module metage2metabo.__main__)
main_cscope() (in module metage2metabo.__main__)
main_iscope() (in module metage2metabo.__main__)
main_metacom() (in module metage2metabo.__main__)
main_mincom() (in module metage2metabo.__main__)
main_recon() (in module metage2metabo.__main__)
main_seeds() (in module metage2metabo.__main__)
main_test() (in module metage2metabo.__main__)
main_workflow() (in module metage2metabo.__main__)
mean_sd_data() (in module metage2metabo.m2m.reconstruction)
merge_html_css_js() (in module metage2metabo.m2m_analysis.graph_compression)
metacom_analysis() (in module metage2metabo.m2m.m2m_workflow)
metage2metabo.__main__
module
metage2metabo.m2m.community_addedvalue
module
metage2metabo.m2m.community_scope
module
metage2metabo.m2m.individual_scope
module
metage2metabo.m2m.m2m_workflow
module
metage2metabo.m2m.minimal_community
module
metage2metabo.m2m.reconstruction
module
metage2metabo.m2m_analysis.enumeration
module
metage2metabo.m2m_analysis.graph_compression
module
metage2metabo.m2m_analysis.m2m_analysis_workflow
module
metage2metabo.m2m_analysis.solution_graph
module
metage2metabo.m2m_analysis.taxonomy
module
metage2metabo.sbml_management
module
metage2metabo.utils
module
mincom() (in module metage2metabo.m2m.minimal_community)
module
metage2metabo.__main__
metage2metabo.m2m.community_addedvalue
metage2metabo.m2m.community_scope
metage2metabo.m2m.individual_scope
metage2metabo.m2m.m2m_workflow
metage2metabo.m2m.minimal_community
metage2metabo.m2m.reconstruction
metage2metabo.m2m_analysis.enumeration
metage2metabo.m2m_analysis.graph_compression
metage2metabo.m2m_analysis.m2m_analysis_workflow
metage2metabo.m2m_analysis.solution_graph
metage2metabo.m2m_analysis.taxonomy
metage2metabo.sbml_management
metage2metabo.utils
P
pgdb_to_sbml() (in module metage2metabo.sbml_management)
powergraph_analysis() (in module metage2metabo.m2m_analysis.graph_compression)
R
recon() (in module metage2metabo.m2m.reconstruction)
reverse_cscope() (in module metage2metabo.m2m.community_scope)
reverse_scope() (in module metage2metabo.m2m.individual_scope)
run_analysis_workflow() (in module metage2metabo.m2m_analysis.m2m_analysis_workflow)
run_pgdb_to_sbml() (in module metage2metabo.sbml_management)
run_workflow() (in module metage2metabo.m2m.m2m_workflow)
S
safe_tar_extract_all() (in module metage2metabo.utils)
T
targets_producibility() (in module metage2metabo.m2m.m2m_workflow)
test_powergraph_heuristics() (in module metage2metabo.m2m_analysis.graph_compression)
U
update_js() (in module metage2metabo.m2m_analysis.graph_compression)
update_js_taxonomy() (in module metage2metabo.m2m_analysis.graph_compression)
update_pathway_tools_xml() (in module metage2metabo.m2m.reconstruction)
update_svg() (in module metage2metabo.m2m_analysis.graph_compression)
update_svg_taxonomy() (in module metage2metabo.m2m_analysis.graph_compression)
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