LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.cfg
medium/DMEM.csv
medium/DMEM.tsv
medium/DMEM_high_FFA.tsv
medium/Hams.tsv
medium/serum.tsv
pipeGEM/__init__.py
pipeGEM/_constant.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/_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/_base.py
pipeGEM/analysis/results/__init__.py
pipeGEM/analysis/results/_base.py
pipeGEM/analysis/results/_file_manager.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/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/cli.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/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/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/DMEM.tsv
pipeGEM/data/medium/DMEM_high_FFA.tsv
pipeGEM/data/medium/Hams.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/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/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/_warning.py
pipeGEM/utils/transform.py
tasks/task_for_Mouse_GEM.json
tasks/tasks.json
tasks/tasks_for_human1.json
tasks/tasks_for_imm1415.json
tasks/tasks_human1.json
tasks/tasks_recon3d.json
tests/__init__.py
tests/conftest.py
tests/test_plotting.py
tests/analysis/__init__.py
tests/analysis/test_consistency.py
tests/analysis/test_flux_analysis.py
tests/analysis/test_model_comp.py
tests/analysis/test_rescaling.py
tests/analysis/test_tasks.py
tests/analysis/test_threshold.py
tests/analysis/results/__init__.py
tests/analysis/results/test_flux_analysis_results.py
tests/cli/__init__.py
tests/cli/test_commands.py
tests/core/__init__.py
tests/core/test_group.py
tests/core/test_model.py
tests/data/__init__.py
tests/data/test_fetching.py
tests/data/test_gene_data.py
tests/data/test_medium_data.py
tests/data/test_synthesis.py
tests/integration/__init__.py
tests/integration/test_CORDA.py
tests/integration/test_MBA.py
tests/integration/test_iMAT.py
tests/integration/test_integrate_gene_data.py
tests/integration/test_mCADRE.py
tests/plotting/__init__.py
tests/plotting/test_heatmap.py
tests/plotting/test_plot_flux.py
tests/plotting/test_scatter.py
tests/utils/__init__.py
tests/utils/test_io.py