GOAT_multi-omics_biomarks / Git / Commit [03aca1]

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GOAT_multi-omics_biomarks

Downloads: 1

Commit [03aca1]

Initial commit

Authored by: AlyssaS 2025-04-19

Browse code at this revision

Parent: [a6d9e5]

Child: [436430]

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added	Dockerfile
added	GO_basic/GO_tree.tsv
added	GO_basic/goa_human.gaf.filt
added	README.md
added	biomarker_discovery.nf
added	data/PPI_human.tsv
added	data/metabolome
added	data/metabolome_HMDB
added	data/proteome
added	environment.yml
added	img/dummy.md
added	img/method_overview.png
added	metPropagate_dir/DAM_cluster.py
added	metPropagate_dir/METABOLOMIC_PROCESSING_PIPELINE/HMDB_ver4_gene_metabolite_annotations.csv
added	metPropagate_dir/integration/assign_z_scores_and_interpret.R
added	metPropagate_dir/integration/generate_labels_met_only.R
added	metPropagate_dir/integration/graph_files/STRING_graph_file_v11_gene_list_functional_entire_db.txt
added	metPropagate_dir/integration/graph_files/STRING_graph_file_v11_gene_to_nodeid_mapping_functional_entire_db.txt
added	metPropagate_dir/integration/graph_files/string_db_percent_of_fn_in_hmdb_weight.csv
added	metPropagate_dir/label_propagation/label_propagation.py
added	metPropagate_dir/label_propagation/main_graph_with_weights.py
added	metPropagate_dir/metProp_result_normalize.py
added	modules/DEomics.py
added	modules/GCN_transformer.py
added	modules/GO_similarity_nwk.py

Dockerfile Diff Switch to side-by-side view

GO_basic/GO_tree.tsv Diff Switch to side-by-side view

GO_basic/goa_human.gaf.filt Diff Switch to side-by-side view

README.md Diff Switch to side-by-side view

biomarker_discovery.nf Diff Switch to side-by-side view

data/PPI_human.tsv Diff Switch to side-by-side view

data/metabolome Diff Switch to side-by-side view

data/metabolome_HMDB Diff Switch to side-by-side view

data/proteome Diff Switch to side-by-side view

environment.yml Diff Switch to side-by-side view

img/dummy.md Diff Switch to side-by-side view

img/method_overview.png

Binary file was added.

metPropagate_dir/DAM_cluster.py Diff Switch to side-by-side view

metPropagate_dir/METABOLOMIC_PROCESSING_PIPELINE/HMDB_ver4_gene_metabolite_annotations.csv Diff Switch to side-by-side view

metPropagate_dir/integration/assign_z_scores_and_interpret.R Diff Switch to side-by-side view

metPropagate_dir/integration/generate_labels_met_only.R Diff Switch to side-by-side view

metPropagate_dir/integration/graph_files/STRING_graph_file_v11_gene_list_functional_entire_db.txt Diff Switch to side-by-side view

metPropagate_dir/integration/graph_files/STRING_graph_file_v11_gene_to_nodeid_mapping_functional_entire_db.txt Diff Switch to side-by-side view

metPropagate_dir/integration/graph_files/string_db_percent_of_fn_in_hmdb_weight.csv Diff Switch to side-by-side view

metPropagate_dir/label_propagation/label_propagation.py Diff Switch to side-by-side view

metPropagate_dir/label_propagation/main_graph_with_weights.py Diff Switch to side-by-side view

metPropagate_dir/metProp_result_normalize.py Diff Switch to side-by-side view

modules/DEomics.py Diff Switch to side-by-side view

modules/GCN_transformer.py Diff Switch to side-by-side view

modules/GO_similarity_nwk.py Diff Switch to side-by-side view

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