LICENSE
MANIFEST.in
README.md
requirements.txt
setup.py
examples/auth_std_libraries/README.md
examples/auth_std_libraries/auth_std_HILIC_pos_12_01_2024_JM_wMS2.csv
examples/auth_std_libraries/auth_std_RP_neg_12_01_2024_JM_wMS2.csv
examples/configurations/khipu_isotopes./up_to_three_groups.json
examples/filters/README.md
examples/filters/drop_dda.json
examples/filters/hilicneg.json
examples/filters/hilicpos.json
examples/filters/qaqc_drop.json
examples/filters/rpneg.json
examples/filters/rppos.json
examples/report_templates/README.md
examples/report_templates/default_batch_corrected.json
examples/report_templates/default_w_tics.json
examples/report_templates/minimal.json
examples/workflows/.DS_Store
examples/workflows/README.md
examples/workflows/bash_workflows/.DS_Store
examples/workflows/bash_workflows/README.md
examples/workflows/bash_workflows/generic/basic_processing_no_AcquireX.sh
examples/workflows/bash_workflows/generic/basic_processing_no_AcquireX_noFilter.sh
examples/workflows/bash_workflows/generic/basic_processing_w_AcquireX.sh
examples/workflows/bash_workflows/generic/minimal_processing.sh
examples/workflows/bash_workflows/generic/two_chromatography_modes_using_filters.sh
examples/workflows/bash_workflows/manuscript/.DS_Store
examples/workflows/bash_workflows/manuscript/Ansone_2021.sh
examples/workflows/bash_workflows/manuscript/Bowen_2023_cell.sh
examples/workflows/bash_workflows/manuscript/Checkmate.sh
examples/workflows/bash_workflows/manuscript/Checkmate_subset.sh
examples/workflows/bash_workflows/manuscript/HZV029_HILIC_subset.sh
examples/workflows/bash_workflows/manuscript/HZV029_QC.sh
examples/workflows/bash_workflows/manuscript/HZV029_RP_subset.sh
examples/workflows/bash_workflows/manuscript/HZV029_plasma_HILIC.sh
examples/workflows/bash_workflows/manuscript/HZV029_plasma_RP.sh
examples/workflows/bash_workflows/manuscript/HZV029_plasma_RP_batch_correct.sh
examples/workflows/bash_workflows/manuscript/HZV029_two_phase_HILIC.sh
examples/workflows/bash_workflows/manuscript/README.md
examples/workflows/bash_workflows/manuscript/bowen_2023_media.sh
examples/workflows/bash_workflows/manuscript/khipu.log
examples/workflows/bash_workflows/manuscript/sequence_files/.DS_Store
examples/workflows/bash_workflows/manuscript/sequence_files/HZV029_Plasma_w_reruns.csv
examples/workflows/bash_workflows/manuscript/sequence_files/HZV029_QC_sequence.csv
examples/workflows/bash_workflows/manuscript/sequence_files/HZV029_TwoPhase.csv
examples/workflows/bash_workflows/manuscript/sequence_files/README.md
examples/workflows/bash_workflows/manuscript/sequence_files/ansone_sequence.csv
examples/workflows/bash_workflows/manuscript/sequence_files/bowen_cell_wo_QC.csv
examples/workflows/bash_workflows/manuscript/sequence_files/bowen_media_wo_QC.csv
examples/workflows/bash_workflows/manuscript/sequence_files/checkmate_orbi_full.csv
examples/workflows/bash_workflows/manuscript/subset_sequence_files/HILIC_pos_subset_sequence.csv
examples/workflows/bash_workflows/manuscript/subset_sequence_files/RP_neg_subset_sequence.csv
examples/workflows/bash_workflows/manuscript/subset_sequence_files/checkmate_orbi_subset_sequence.csv
examples/workflows/nextflow/README.md
examples/workflows/nextflow/minimal_nextflow.nf
examples/workflows/nextflow/nextflow
examples/workflows/nextflow/process_w_filter_w_acquireX.nf
examples/workflows/nextflow/compatible_workflows/basic_process_w_filter_w_acquireX.sh
examples/workflows/nextflow/compatible_workflows/example_filter_acquirex_jobs.csv
examples/workflows/nextflow/compatible_workflows/example_input_minimal_jobs.csv
examples/workflows/nextflow/compatible_workflows/minimal_processing.sh
jms_hack/__init__.py
jms_hack/coverage.py
jms_hack/dbStructures.py
jms_hack/empiricalCpds.py
jms_hack/formula.py
jms_hack/io.py
jms_hack/ions.py
jms_hack/modelConvert.py
jms_hack/model_port.py
jms_hack/search.py
jms_hack/test.py
jms_hack/updates.py
jms_hack/data/__init__.py
jms_hack/data/humangem_pathways.py
jms_hack/data/list_formula_mass.py
jms_hack/data/masters.py
jms_hack/data/smpdb_pathways.py
jms_hack/utils/Tabular2Json.py
jms_hack/utils/__init__.py
jms_hack/utils/chemebi.py
jms_hack/utils/gems.py
jms_hack/utils/hmdb.py
jms_hack/utils/pubchem.py
jms_hack/utils/refmet.py
pcpfm/Acquisition.py
pcpfm/EmpCpds.py
pcpfm/Experiment.py
pcpfm/FeatureTable.py
pcpfm/MSnSpectrum.py
pcpfm/Report.py
pcpfm/__init__.py
pcpfm/__main__.py
pcpfm/default_parameters.py
pcpfm/main.py
pcpfm/utils.py
pcpfm.egg-info/PKG-INFO
pcpfm.egg-info/SOURCES.txt
pcpfm.egg-info/dependency_links.txt
pcpfm.egg-info/entry_points.txt
pcpfm.egg-info/requires.txt
pcpfm.egg-info/top_level.txt
pcpfm/annotation_sources/README.md
pcpfm/default_configs/__init__.py
pcpfm/default_configs/default_adducts_neg_feature.json
pcpfm/default_configs/default_adducts_neg_khipu.json
pcpfm/default_configs/default_adducts_pos_feature.json
pcpfm/default_configs/default_adducts_pos_khipu.json
pcpfm/default_configs/default_auto_drop.json
pcpfm/default_configs/default_charges.json
pcpfm/default_configs/default_experiment_params.json
pcpfm/default_configs/default_extended_adducts.json
pcpfm/default_configs/default_isotopes.json
pcpfm/default_configs/default_preprocessing.json
pcpfm/default_configs/default_report.json
pcpfm/default_configs/hzv029_report.json