LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.cfg
pipeGEM/__init__.py
pipeGEM/_constant.py
pipeGEM/_logging.py
pipeGEM/exceptions.py
pipeGEM.egg-info/PKG-INFO
pipeGEM.egg-info/SOURCES.txt
pipeGEM.egg-info/dependency_links.txt
pipeGEM.egg-info/entry_points.txt
pipeGEM.egg-info/requires.txt
pipeGEM.egg-info/top_level.txt
pipeGEM/analysis/__init__.py
pipeGEM/analysis/_auto_stat.py
pipeGEM/analysis/_consistency.py
pipeGEM/analysis/_dim_reduction.py
pipeGEM/analysis/_flux.py
pipeGEM/analysis/_gapsplit.py
pipeGEM/analysis/_ko.py
pipeGEM/analysis/_mapping.py
pipeGEM/analysis/_problem.py
pipeGEM/analysis/_reducing.py
pipeGEM/analysis/_stat.py
pipeGEM/analysis/_threshold.py
pipeGEM/analysis/_utils.py
pipeGEM/analysis/graph/__init__.py
pipeGEM/analysis/graph/_transform.py
pipeGEM/analysis/lp/_FASTCORE.py
pipeGEM/analysis/lp/_SWIFTCORE.py
pipeGEM/analysis/lp/__init__.py
pipeGEM/analysis/pathway/__init__.py
pipeGEM/analysis/pathway/_analysis.py
pipeGEM/analysis/pathway/_base.py
pipeGEM/analysis/pathway/_kegg.py
pipeGEM/analysis/results/__init__.py
pipeGEM/analysis/results/_base.py
pipeGEM/analysis/results/_file_manager.py
pipeGEM/analysis/results/auto_stat.py
pipeGEM/analysis/results/consistency.py
pipeGEM/analysis/results/corr.py
pipeGEM/analysis/results/data.py
pipeGEM/analysis/results/dim_reduction.py
pipeGEM/analysis/results/ec.py
pipeGEM/analysis/results/flux_analysis.py
pipeGEM/analysis/results/group_comp.py
pipeGEM/analysis/results/integration.py
pipeGEM/analysis/results/ko_analysis.py
pipeGEM/analysis/results/scaling.py
pipeGEM/analysis/results/stat.py
pipeGEM/analysis/results/task.py
pipeGEM/analysis/results/thresholds.py
pipeGEM/analysis/scaling/__init__.py
pipeGEM/analysis/scaling/_base.py
pipeGEM/analysis/scaling/_scalers.py
pipeGEM/analysis/tasks/__init__.py
pipeGEM/analysis/tasks/_base.py
pipeGEM/analysis/tasks/_var.py
pipeGEM/analysis/tasks/gapfill.py
pipeGEM/analysis/tasks/task_files/tasks_for_imm1415.json
pipeGEM/analysis/tasks/task_files/tasks_human1.json
pipeGEM/analysis/tasks/task_files/tasks_recon3d.json
pipeGEM/cli/__init__.py
pipeGEM/cli/__main__.py
pipeGEM/cli/_doc.py
pipeGEM/cli/_io.py
pipeGEM/cli/_utils.py
pipeGEM/cli/_validation.py
pipeGEM/cli/cli.py
pipeGEM/cli/errors.py
pipeGEM/cli/config/__init__.py
pipeGEM/cli/config/base.py
pipeGEM/cli/config/pipeline.py
pipeGEM/cli/config/types.py
pipeGEM/cli/configs/comparison.toml
pipeGEM/cli/configs/gene_data.toml
pipeGEM/cli/configs/mapping.toml
pipeGEM/cli/configs/model.toml
pipeGEM/cli/configs/multi_model.toml
pipeGEM/cli/configs/flux_analysis/pFBA.toml
pipeGEM/cli/configs/gene_data_integration/CORDA.toml
pipeGEM/cli/configs/gene_data_integration/EFlux.toml
pipeGEM/cli/configs/gene_data_integration/GIMME.toml
pipeGEM/cli/configs/gene_data_integration/INIT.toml
pipeGEM/cli/configs/gene_data_integration/MBA.toml
pipeGEM/cli/configs/gene_data_integration/RIPTiDe_sampling.toml
pipeGEM/cli/configs/gene_data_integration/iMAT.toml
pipeGEM/cli/configs/gene_data_integration/mCADRE.toml
pipeGEM/cli/configs/gene_data_integration/rFASTCORMICS.toml
pipeGEM/cli/configs/thresholds/local_threshold.toml
pipeGEM/cli/configs/thresholds/percentile_threshold.toml
pipeGEM/cli/configs/thresholds/rFASTCORMICS_threshold.toml
pipeGEM/cli/pipelines/__init__.py
pipeGEM/cli/pipelines/base.py
pipeGEM/cli/pipelines/comparison.py
pipeGEM/cli/pipelines/flux.py
pipeGEM/cli/pipelines/integration.py
pipeGEM/cli/pipelines/model_processing.py
pipeGEM/cli/pipelines/template.py
pipeGEM/cli/pipelines/threshold.py
pipeGEM/core/__init__.py
pipeGEM/core/_base.py
pipeGEM/core/_group.py
pipeGEM/core/_model.py
pipeGEM/data/__init__.py
pipeGEM/data/_base.py
pipeGEM/data/data.py
pipeGEM/data/fetching.py
pipeGEM/data/medium_registry.py
pipeGEM/data/preprocessing.py
pipeGEM/data/synthesis.py
pipeGEM/data/thermal.py
pipeGEM/data/enzyme_data/kcat.csv
pipeGEM/data/enzyme_data/mw.csv
pipeGEM/data/enzyme_data/human/human-gem.csv
pipeGEM/data/medium/BHI.tsv
pipeGEM/data/medium/CGXII.tsv
pipeGEM/data/medium/DMEM.tsv
pipeGEM/data/medium/DMEM_high_FFA.tsv
pipeGEM/data/medium/Hams.tsv
pipeGEM/data/medium/LB.tsv
pipeGEM/data/medium/M63.tsv
pipeGEM/data/medium/M9.tsv
pipeGEM/data/medium/MOPS.tsv
pipeGEM/data/medium/R2A.tsv
pipeGEM/data/medium/SOC.tsv
pipeGEM/data/medium/TB.tsv
pipeGEM/data/medium/serum.tsv
pipeGEM/extensions/__init__.py
pipeGEM/extensions/DLKcat/__init__.py
pipeGEM/extensions/DLKcat/data.py
pipeGEM/extensions/DLKcat/main.py
pipeGEM/extensions/DLKcat/model.py
pipeGEM/extensions/DLKcat/preprocess.py
pipeGEM/extensions/DLKcat/utils.py
pipeGEM/extensions/DLKcat/precomputed_obj/atom_dict.pickle
pipeGEM/extensions/DLKcat/precomputed_obj/bond_dict.pickle
pipeGEM/extensions/DLKcat/precomputed_obj/edge_dict.pickle
pipeGEM/extensions/DLKcat/precomputed_obj/fingerprint_dict.pickle
pipeGEM/extensions/DLKcat/precomputed_obj/model_state
pipeGEM/extensions/DLKcat/precomputed_obj/sequence_dict.pickle
pipeGEM/integration/__init__.py
pipeGEM/integration/_class.py
pipeGEM/integration/algo/CORDA.py
pipeGEM/integration/algo/FASTCORE.py
pipeGEM/integration/algo/INIT.py
pipeGEM/integration/algo/MBA.py
pipeGEM/integration/algo/SWIFTCORE.py
pipeGEM/integration/algo/__init__.py
pipeGEM/integration/algo/ftINIT.py
pipeGEM/integration/algo/iMAT.py
pipeGEM/integration/algo/mCADRE.py
pipeGEM/integration/algo/rFASTCORMICS.py
pipeGEM/integration/continuous/Eflux.py
pipeGEM/integration/continuous/GIMME.py
pipeGEM/integration/continuous/RIPTiDe.py
pipeGEM/integration/continuous/SPOT.py
pipeGEM/integration/continuous/__init__.py
pipeGEM/integration/ec/__init__.py
pipeGEM/integration/ec/_builder.py
pipeGEM/integration/ec/_copy.py
pipeGEM/integration/ec/autopacmen.py
pipeGEM/integration/ec/gecko_full.py
pipeGEM/integration/ec/gecko_light.py
pipeGEM/integration/ec/utils.py
pipeGEM/integration/regulatory/PROM.py
pipeGEM/integration/regulatory/TRFBA.py
pipeGEM/integration/regulatory/__init__.py
pipeGEM/integration/utils/__init__.py
pipeGEM/integration/utils/_problem.py
pipeGEM/integration/utils/_thresholds.py
pipeGEM/plotting/__init__.py
pipeGEM/plotting/_class.py
pipeGEM/plotting/_flux.py
pipeGEM/plotting/_prep.py
pipeGEM/plotting/_utils.py
pipeGEM/plotting/categorical.py
pipeGEM/plotting/curve.py
pipeGEM/plotting/heatmap.py
pipeGEM/plotting/scatter.py
pipeGEM/utils/__init__.py
pipeGEM/utils/_calc.py
pipeGEM/utils/_class.py
pipeGEM/utils/_io.py
pipeGEM/utils/_manipulate.py
pipeGEM/utils/_scaling.py
pipeGEM/utils/_selection.py
pipeGEM/utils/_validators.py
pipeGEM/utils/_warning.py
pipeGEM/utils/transform.py
tests/test_plotting.py