LICENSE
MANIFEST.in
README.md
history.md
requirements.txt
setup.cfg
setup.py
examples/input/demo_map_proteinfamilies.ident50.tsv
examples/input/demo_proteinfamilies.DDI.simple.tsv
examples/input/demo_proteinfamilies.GO.homology.tsv
examples/input/demo_proteinfamilies.GO.simple.tsv
examples/input/demo_proteinfamilies.GO.tsv
examples/input/demo_proteinfamilies.contig.simple.tsv
examples/input/demo_proteinfamilies_rna_CPM.stratified_Species_mtx.tsv
examples/output/fugassem_input_prep/demo.proteinfamilies.nrm.tsv
examples/output/fugassem_input_prep/demo_proteinfamilies.DDI.simple.tsv
examples/output/fugassem_input_prep/demo_proteinfamilies.GO.homology.tsv
examples/output/fugassem_input_prep/demo_proteinfamilies.GO.simple.tsv
examples/output/fugassem_input_prep/demo_proteinfamilies.contig.simple.tsv
examples/output/fugassem_output/Ecoli.coexp_ML.GO0005886.auc.png
examples/output/fugassem_output/Ecoli.finalized_ML.GO0005886.auc.png
examples/output/fugassem_output/demo_GO.Escherichia_coli.coexp_ML.each.auc.pdf
examples/output/fugassem_output/demo_GO.Escherichia_coli.finalized_ML.each.auc.pdf
examples/output/fugassem_output/demo_GO.coexp_ML.prediction.tsv
examples/output/fugassem_output/demo_GO.finalized_ML.prediction.tsv
examples/output/fugassem_output/demo_GO.matrix1_ML.prediction.tsv
examples/output/fugassem_output/demo_GO.matrix2_ML.prediction.tsv
examples/output/fugassem_output/demo_GO.vector1_ML.prediction.tsv
examples/output/fugassem_output_bug_specific/demo_GO.finalized_ML.prediction.tsv
examples/output/fugassem_output_mtx/demo_GO.finalized_ML.prediction.tsv
examples/output/fugassem_output_union/demo_GO.finalized_ML.prediction.tsv
examples/output/fugassem_output_union_advanced/demo_GO.finalized_ML.prediction.tsv
examples/output/fugassem_output_universal/demo_GO.finalized_ML.prediction.tsv
examples/raw_input/demo_gene_info.tsv
examples/raw_input/demo_genecatalogs.centroid.fna
examples/raw_input/demo_genecatalogs.clstr
examples/raw_input/demo_map_proteinfamilies.ident50.tsv
examples/raw_input/demo_proteinfamilies.clstr
examples/raw_input/demo_proteinfamilies_annotation.taxonomy.tsv
examples/raw_input/demo_proteinfamilies_annotation.tsv
examples/raw_input/sample1.R1.fastq.gz
examples/raw_input/sample1.R2.fastq.gz
examples/raw_input/sample2.R1.fastq.gz
examples/raw_input/sample2.R2.fastq.gz
fugassem/__init__.py
fugassem/config.py
fugassem/fugassem.py
fugassem/utilities.py
fugassem.egg-info/PKG-INFO
fugassem.egg-info/SOURCES.txt
fugassem.egg-info/dependency_links.txt
fugassem.egg-info/entry_points.txt
fugassem.egg-info/not-zip-safe
fugassem.egg-info/top_level.txt
fugassem/common/__init__.py
fugassem/common/corrmp.py
fugassem/common/dictation.py
fugassem/common/extract_feature_subset.py
fugassem/common/format_function.py
fugassem/common/geneontology.py
fugassem/common/table2.py
fugassem/common/table2_stats.py
fugassem/common/transpose.py
fugassem/common/utils.py
fugassem/data/GO/go-basic.obo
fugassem/data/GO/go.obo.gz
fugassem/predict/__init__.py
fugassem/predict/collect_ml_results.py
fugassem/predict/machine_learning.py
fugassem/predict/merged_prediction.py
fugassem/predict/predict_function.py
fugassem/predict/prepare_nextlayer_ml.py
fugassem/predict/select_feature.py
fugassem/preprocess/__init__.py
fugassem/preprocess/build_union_terms.py
fugassem/preprocess/calculate_correlation.py
fugassem/preprocess/collect_features.py
fugassem/preprocess/convert_coann.py
fugassem/preprocess/impute_nan.py
fugassem/preprocess/refine_abunds.py
fugassem/preprocess/refine_anns.py
fugassem/preprocess/split_taxa.py
fugassem/tasks/__init__.py
fugassem/tasks/fugassem_prediction.py
fugassem/tasks/fugassem_preprocessing.py
fugassem/tasks/fugassem_process.py
fugassem/tools/__init__.py
fugassem/tools/abundance_RPK.py
fugassem/tools/abundance_normalization.py
fugassem/tools/abundance_smoothing.py
fugassem/tools/collect_seqSimilarity_results.py
fugassem/tools/extract_feature_subset.py
fugassem/tools/gene_abundance.py
fugassem/tools/gene_abundance_indexRef.py
fugassem/tools/gene_catalog_abundance.py
fugassem/tools/generate_annotation_input.py
fugassem/tools/generate_stratified_mtx_input.py
fugassem/tools/performance_vis.py
fugassem/tools/prepare_annotation.py
fugassem/tools/prepare_coann_pairs.py
fugassem/tools/prepare_contig.py
fugassem/tools/prepare_seqSimilarity.py
fugassem/tools/stratified_abundance.py
fugassem/tools/sum_to_family_abundance.py
fugassem/workflows/fugassem_workflow.py