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config.yaml
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config.yaml
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# Connection to Neo4j database
neo4j_id: 'neo4j' # default
neo4j_password: '4jneo'
database: "bolt://localhost:7687"
# To find the appropriate database address: from Neo4j standalone,
# start the database and via the "Manage" track, go to "Details",
# then check the IP adress and Bolt port
# Folder containing input clustering results
clusterings_folder: "./data"
# Specify the label to identify object nodes in the graph
object_nodes_name: 'Patient'
# Specify the label to identify cluster nodes in the graph
cluster_nodes_name: 'Cluster'
# If False return only objects that pass all filters (i.e, not reassigned patients)
# If True, but reassign_unclassified set to False, small clusters won't be removed from the final clustering
## and patients that never reach high enough number of supports will be outputed in a cluster labelled 'unclassified'
write_all: 'True'
# If set to True, ClustOmics will try to assign filtered out objects to consensus clusters
# Ignored if write_all is set to False
reassign_unclassified: 'True'
# For each Integration Edge, specify the datatypes to merge
# RELATION_NAME: 'datatype1|datatype2|...|datatypeN'
datatypes:
# AML Multi-to-Multi
AML_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 'multiomics'
# AML Single-to-Multi OnlyMulti
AML_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 'expression|methylation|mirna'
# AML Single-to-Multi All
AML_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 'expression|methylation|mirna'
# COAD Multi-to-Multi
COAD_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 'multiomics'
# COAD Single-to-Multi OnlyMulti
COAD_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 'expression|methylation|mirna'
# COAD Single-to-Multi All
COAD_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 'expression|methylation|mirna'
# BIC Multi-to-Multi
BIC_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 'multiomics'
# BIC Single-to-Multi OnlyMulti
BIC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 'expression|methylation|mirna'
# BIC Single-to-Multi All
BIC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 'expression|methylation|mirna'
# GBM Multi-to-Multi
GBM_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 'multiomics'
# GBM Single-to-Multi OnlyMulti
GBM_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 'expression|methylation|mirna'
# GBM Single-to-Multi All
GBM_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 'expression|methylation|mirna'
# KIRC Multi-to-Multi
KIRC_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 'multiomics'
# KIRC Single-to-Multi OnlyMulti
KIRC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 'expression|methylation|mirna'
# KIRC Single-to-Multi All
KIRC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 'expression|methylation|mirna'
# OV Multi-to-Multi
OV_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 'multiomics'
# OV Single-to-Multi OnlyMulti
OV_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 'expression|methylation|mirna'
# OV Single-to-Multi All
OV_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 'expression|methylation|mirna'
# SARC Multi-to-Multi
SARC_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 'multiomics'
# SARC Single-to-Multi OnlyMulti
SARC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 'expression|methylation|mirna'
# SARC Single-to-Multi All
SARC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 'expression|methylation|mirna'
# LUSC Multi-to-Multi
LUSC_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 'multiomics'
# LUSC Single-to-Multi OnlyMulti
LUSC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 'expression|methylation|mirna'
# LUSC Single-to-Multi All
LUSC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 'expression|methylation|mirna'
# LIHC Multi-to-Multi
LIHC_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 'multiomics'
# LIHC Single-to-Multi OnlyMulti
LIHC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 'expression|methylation|mirna'
# LIHC Single-to-Multi All
LIHC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 'expression|methylation|mirna'
# SARC Multi-to-Multi
SARC_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 'multiomics'
# SARC Single-to-Multi OnlyMulti
SARC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 'expression|methylation|mirna'
# SARC Single-to-Multi All
SARC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 'expression|methylation|mirna'
# SKCM Multi-to-Multi
SKCM_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 'multiomics'
# SKCM Single-to-Multi OnlyMulti
SKCM_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 'expression|methylation|mirna'
# SKCM Single-to-Multi All
SKCM_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 'expression|methylation|mirna'
# For each Integration Edge, specify the methods to merge
# RELATION_NAME: 'method1|method2|...|methodN'
methods:
AML_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 'MCCA|PINS|NEMO|SNF|rMKL'
AML_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 'PINS|NEMO|SNF|rMKL|kmeans'
AML_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 'PINS|NEMO|SNF|rMKL|kmeans'
COAD_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 'MCCA|PINS|NEMO|SNF|rMKL'
COAD_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 'PINS|NEMO|SNF|rMKL|kmeans'
COAD_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 'PINS|NEMO|SNF|rMKL|kmeans'
BIC_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 'MCCA|PINS|NEMO|SNF|rMKL'
BIC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 'PINS|NEMO|SNF|rMKL|kmeans'
BIC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 'PINS|NEMO|SNF|rMKL|kmeans'
GBM_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 'MCCA|PINS|NEMO|SNF|rMKL'
GBM_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 'PINS|NEMO|SNF|rMKL|kmeans'
GBM_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 'PINS|NEMO|SNF|rMKL|kmeans'
KIRC_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 'MCCA|PINS|NEMO|SNF|rMKL'
KIRC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 'PINS|NEMO|SNF|rMKL|kmeans'
KIRC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 'PINS|NEMO|SNF|rMKL|kmeans'
OV_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 'MCCA|PINS|NEMO|SNF|rMKL'
OV_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 'PINS|NEMO|SNF|rMKL|kmeans'
OV_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 'PINS|NEMO|SNF|rMKL|kmeans'
SARC_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 'MCCA|PINS|NEMO|SNF|rMKL'
SARC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 'PINS|NEMO|SNF|rMKL|kmeans'
SARC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 'PINS|NEMO|SNF|rMKL|kmeans'
LUSC_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 'MCCA|PINS|NEMO|SNF|rMKL'
LUSC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 'PINS|NEMO|SNF|rMKL|kmeans'
LUSC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 'PINS|NEMO|SNF|rMKL|kmeans'
LIHC_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 'MCCA|PINS|NEMO|SNF|rMKL'
LIHC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 'PINS|NEMO|SNF|rMKL|kmeans'
LIHC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 'PINS|NEMO|SNF|rMKL|kmeans'
SKCM_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 'MCCA|PINS|NEMO|SNF|rMKL'
SKCM_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 'PINS|NEMO|SNF|rMKL|kmeans'
SKCM_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 'PINS|NEMO|SNF|rMKL|kmeans'
# For each Integration Edge, specify the minimum allowed size for clusters
# Clusters containing less than x nodes will be removed from the analysis
# Must be a positive integer
min_size_clust:
AML_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 8
AML_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 8
AML_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 8
BIC_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 8
BIC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 8
BIC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 31
COAD_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 8
COAD_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 8
COAD_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 11
GBM_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 8
GBM_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 8
GBM_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 13
KIRC_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 8
KIRC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 8
KIRC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 9
LIHC_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 8
LIHC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 8
LIHC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 18
LUSC_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 8
LUSC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 8
LUSC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 17
OV_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 8
OV_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 8
OV_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 14
SARC_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 8
SARC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 8
SARC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 12
SKCM_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 8
SKCM_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 8
SKCM_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 17
# For each Integration Edge, specify the minimum number of objects to be returned
# This parameters is only used when the number of supports to use to filter the graph is not specified
min_size_consensus:
AML_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 161
AML_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 161
AML_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 161
BIC_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 589
BIC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 589
BIC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 589
COAD_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 209
COAD_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 209
COAD_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 209
GBM_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 260
GBM_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 260
GBM_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 260
KIRC_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 173
KIRC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 173
KIRC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 173
LIHC_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 348
LIHC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 348
LIHC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 348
LUSC_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 323
LUSC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 323
LUSC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 323
OV_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 272
OV_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 272
OV_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 272
SARC_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 244
SARC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 244
SARC_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 244
SKCM_MULTI_MCCA_NEMO_PINS_SNF_rMKL: 333
SKCM_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans: 333
SKCM_EXP_MIRNA_MET_NEMO_PINS_SNF_rMKL_kmeans_all: 333