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idekerlab / pyNBS Public

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pyNBS Command Line Execution

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Tongqiu (Iris) Jia edited this page Jan 11, 2018 · 1 revision

Run pyNBS from command line

Toggle table of contents Pages 50

Home
Installing pyNBS
Molecular Network File Format
Patient Survival Data File Format
pyNBS Command Line Execution
pyNBS Command Line Manual
pyNBS Jupyter Notebook Examples
pyNBS Parameters File
pyNBS.consensus_clustering
pyNBS.consensus_clustering.consensus_hclust_hard
pyNBS.consensus_clustering.Hlist_constructor_from_folder
pyNBS.data_import_tools
pyNBS.data_import_tools.degree_shuffNet
pyNBS.data_import_tools.filter_weighted_network
pyNBS.data_import_tools.label_shuffNet
pyNBS.data_import_tools.load_binary_mutation_data
pyNBS.data_import_tools.load_network_file
pyNBS.data_import_tools.load_params
pyNBS.data_import_tools.process_TCGA_MAF
pyNBS.gene_conversion_tools
pyNBS.gene_conversion_tools.construct_query_map_table
pyNBS.gene_conversion_tools.convert_custom_namelist
pyNBS.gene_conversion_tools.convert_edgelist
pyNBS.gene_conversion_tools.exclude_id
pyNBS.gene_conversion_tools.filter_converted_edgelist
pyNBS.gene_conversion_tools.filter_query_edgelist
pyNBS.gene_conversion_tools.get_identifier_without_prefix
pyNBS.gene_conversion_tools.query_batch
pyNBS.gene_conversion_tools.query_constructor
pyNBS.gene_conversion_tools.write_edgelist
pyNBS.network_propagation
pyNBS.network_propagation.fast_random_walk
pyNBS.network_propagation.network_kernel_propagation
pyNBS.network_propagation.network_propagation
pyNBS.network_propagation.normalize_network
pyNBS.pyNBS_core
pyNBS.pyNBS_core.mixed_netNMF
pyNBS.pyNBS_core.mixed_netNMF_debug
pyNBS.pyNBS_core.network_inf_KNN_glap
pyNBS.pyNBS_core.qnorm
pyNBS.pyNBS_core.subsample_sm_mat
pyNBS.pyNBS_plotting
pyNBS.pyNBS_plotting.cluster_color_assign
pyNBS.pyNBS_plotting.cluster_KMplot
pyNBS.pyNBS_plotting.plot_cc_map
pyNBS.pyNBS_single
pyNBS.pyNBS_single.NBS_single
Somatic Mutation Data File Format
Supplemental Information and Analysis
The pyNBS Algorithm

Home

Running pyNBS

Installation
Command Line
Jupyter Notebook

pyNBS Algorithm

pyNBS Modules

consensus_clustering
data_import_tools
gene_conversion_tools
network_propagation
pyNBS_core
pyNBS_single
pyNBS_plotting

pyNBS Supplement

Appendix

Molecular Network File
pyNBS Parameters File
Patient Survival Data File
Somatic Mutation Data File

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