├── .gitignore ├── LICENSE ├── LipidFinder ├── Amalgamator │ └── __init__.py ├── Configuration │ ├── LFParametersCLI.py │ ├── LFParametersGUI.py │ └── __init__.py ├── Data │ ├── adducts_negative.csv │ ├── adducts_positive.csv │ ├── contaminants_negative.csv │ ├── contaminants_positive.csv │ ├── ionfragments_negative.csv │ ├── ionfragments_positive.csv │ ├── md_inclusion_negative.csv │ ├── md_inclusion_positive.csv │ ├── parameters_template.json │ └── stacks.csv ├── LFDataFrame.py ├── MSSearch │ ├── DataPlots.py │ ├── Summary.py │ └── __init__.py ├── PeakFilter │ ├── BroadContaminant.py │ ├── Clustering.py │ ├── ContaminantRemoval.py │ ├── Deisotoping.py │ ├── FalseDiscoveryRate.py │ ├── InSrcFragRemoval.py │ ├── MassDefectFilter.py │ ├── MassReassignment.py │ ├── OutlierCorrection.py │ ├── PeakFinder.py │ ├── QCCalcs.py │ ├── RTCorrection.py │ ├── SampleMeansCalc.py │ ├── SolventCalcs.py │ ├── Summary.py │ └── __init__.py ├── __init__.py ├── _py3k │ └── __init__.py ├── _utils │ └── __init__.py ├── config_params.py ├── run_amalgamator.py ├── run_mssearch.py ├── run_peakfilter.py └── update_params.py ├── MANIFEST.in ├── README.md ├── docs ├── Input_preparation_manual.pdf ├── LipidFinder2_manual.ipynb ├── LipidFinder2_manual.pdf ├── PeakFilter_stages_information.pdf ├── sources │ ├── Input_preparation_manual.docx │ ├── LipidFinder2_manual.ipynb │ ├── PeakFilter_stages_information.docx │ ├── my_bibliography.bib │ └── my_template.tplx └── xcms.R ├── requirements.txt ├── setup.py └── tests ├── LipidFinder-1.0 ├── old_adducts.csv └── old_parameters.csv ├── SIEVE ├── params_amalgamator.json ├── params_mssearch.json ├── params_peakfilter_negative.json ├── params_peakfilter_positive.json ├── sieve_negative.csv └── sieve_positive.csv └── XCMS ├── params_amalgamator.json ├── params_mssearch.json ├── params_peakfilter_negative.json ├── params_peakfilter_positive.json ├── xcms_negative.csv └── xcms_positive.csv /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LICENSE -------------------------------------------------------------------------------- /LipidFinder/Amalgamator/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/Amalgamator/__init__.py -------------------------------------------------------------------------------- /LipidFinder/Configuration/LFParametersCLI.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/Configuration/LFParametersCLI.py -------------------------------------------------------------------------------- /LipidFinder/Configuration/LFParametersGUI.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/Configuration/LFParametersGUI.py -------------------------------------------------------------------------------- /LipidFinder/Configuration/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/Configuration/__init__.py -------------------------------------------------------------------------------- /LipidFinder/Data/adducts_negative.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/Data/adducts_negative.csv -------------------------------------------------------------------------------- /LipidFinder/Data/adducts_positive.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/Data/adducts_positive.csv -------------------------------------------------------------------------------- /LipidFinder/Data/contaminants_negative.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/Data/contaminants_negative.csv -------------------------------------------------------------------------------- /LipidFinder/Data/contaminants_positive.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/Data/contaminants_positive.csv -------------------------------------------------------------------------------- /LipidFinder/Data/ionfragments_negative.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/Data/ionfragments_negative.csv -------------------------------------------------------------------------------- /LipidFinder/Data/ionfragments_positive.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/Data/ionfragments_positive.csv -------------------------------------------------------------------------------- /LipidFinder/Data/md_inclusion_negative.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/Data/md_inclusion_negative.csv -------------------------------------------------------------------------------- /LipidFinder/Data/md_inclusion_positive.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/Data/md_inclusion_positive.csv -------------------------------------------------------------------------------- /LipidFinder/Data/parameters_template.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/Data/parameters_template.json -------------------------------------------------------------------------------- /LipidFinder/Data/stacks.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/Data/stacks.csv -------------------------------------------------------------------------------- /LipidFinder/LFDataFrame.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/LFDataFrame.py -------------------------------------------------------------------------------- /LipidFinder/MSSearch/DataPlots.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/MSSearch/DataPlots.py -------------------------------------------------------------------------------- /LipidFinder/MSSearch/Summary.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/MSSearch/Summary.py -------------------------------------------------------------------------------- /LipidFinder/MSSearch/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/MSSearch/__init__.py -------------------------------------------------------------------------------- /LipidFinder/PeakFilter/BroadContaminant.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/PeakFilter/BroadContaminant.py -------------------------------------------------------------------------------- /LipidFinder/PeakFilter/Clustering.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/PeakFilter/Clustering.py -------------------------------------------------------------------------------- /LipidFinder/PeakFilter/ContaminantRemoval.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/PeakFilter/ContaminantRemoval.py -------------------------------------------------------------------------------- /LipidFinder/PeakFilter/Deisotoping.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/PeakFilter/Deisotoping.py -------------------------------------------------------------------------------- /LipidFinder/PeakFilter/FalseDiscoveryRate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/PeakFilter/FalseDiscoveryRate.py -------------------------------------------------------------------------------- /LipidFinder/PeakFilter/InSrcFragRemoval.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/PeakFilter/InSrcFragRemoval.py -------------------------------------------------------------------------------- /LipidFinder/PeakFilter/MassDefectFilter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/PeakFilter/MassDefectFilter.py -------------------------------------------------------------------------------- /LipidFinder/PeakFilter/MassReassignment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/PeakFilter/MassReassignment.py -------------------------------------------------------------------------------- /LipidFinder/PeakFilter/OutlierCorrection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/PeakFilter/OutlierCorrection.py -------------------------------------------------------------------------------- /LipidFinder/PeakFilter/PeakFinder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/PeakFilter/PeakFinder.py -------------------------------------------------------------------------------- /LipidFinder/PeakFilter/QCCalcs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/PeakFilter/QCCalcs.py -------------------------------------------------------------------------------- /LipidFinder/PeakFilter/RTCorrection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/PeakFilter/RTCorrection.py -------------------------------------------------------------------------------- /LipidFinder/PeakFilter/SampleMeansCalc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/PeakFilter/SampleMeansCalc.py -------------------------------------------------------------------------------- /LipidFinder/PeakFilter/SolventCalcs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/PeakFilter/SolventCalcs.py -------------------------------------------------------------------------------- /LipidFinder/PeakFilter/Summary.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/PeakFilter/Summary.py -------------------------------------------------------------------------------- /LipidFinder/PeakFilter/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/PeakFilter/__init__.py -------------------------------------------------------------------------------- /LipidFinder/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/__init__.py -------------------------------------------------------------------------------- /LipidFinder/_py3k/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/_py3k/__init__.py -------------------------------------------------------------------------------- /LipidFinder/_utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/_utils/__init__.py -------------------------------------------------------------------------------- /LipidFinder/config_params.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/config_params.py -------------------------------------------------------------------------------- /LipidFinder/run_amalgamator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/run_amalgamator.py -------------------------------------------------------------------------------- /LipidFinder/run_mssearch.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/run_mssearch.py -------------------------------------------------------------------------------- /LipidFinder/run_peakfilter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/run_peakfilter.py -------------------------------------------------------------------------------- /LipidFinder/update_params.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/LipidFinder/update_params.py -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/README.md -------------------------------------------------------------------------------- /docs/Input_preparation_manual.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/docs/Input_preparation_manual.pdf -------------------------------------------------------------------------------- /docs/LipidFinder2_manual.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/docs/LipidFinder2_manual.ipynb -------------------------------------------------------------------------------- /docs/LipidFinder2_manual.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/docs/LipidFinder2_manual.pdf -------------------------------------------------------------------------------- /docs/PeakFilter_stages_information.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/docs/PeakFilter_stages_information.pdf -------------------------------------------------------------------------------- /docs/sources/Input_preparation_manual.docx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/docs/sources/Input_preparation_manual.docx -------------------------------------------------------------------------------- /docs/sources/LipidFinder2_manual.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/docs/sources/LipidFinder2_manual.ipynb -------------------------------------------------------------------------------- /docs/sources/PeakFilter_stages_information.docx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/docs/sources/PeakFilter_stages_information.docx -------------------------------------------------------------------------------- /docs/sources/my_bibliography.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/docs/sources/my_bibliography.bib -------------------------------------------------------------------------------- /docs/sources/my_template.tplx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/docs/sources/my_template.tplx -------------------------------------------------------------------------------- /docs/xcms.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/docs/xcms.R -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/requirements.txt -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/setup.py -------------------------------------------------------------------------------- /tests/LipidFinder-1.0/old_adducts.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/tests/LipidFinder-1.0/old_adducts.csv -------------------------------------------------------------------------------- /tests/LipidFinder-1.0/old_parameters.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/tests/LipidFinder-1.0/old_parameters.csv -------------------------------------------------------------------------------- /tests/SIEVE/params_amalgamator.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/tests/SIEVE/params_amalgamator.json -------------------------------------------------------------------------------- /tests/SIEVE/params_mssearch.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/tests/SIEVE/params_mssearch.json -------------------------------------------------------------------------------- /tests/SIEVE/params_peakfilter_negative.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/tests/SIEVE/params_peakfilter_negative.json -------------------------------------------------------------------------------- /tests/SIEVE/params_peakfilter_positive.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/tests/SIEVE/params_peakfilter_positive.json -------------------------------------------------------------------------------- /tests/SIEVE/sieve_negative.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/tests/SIEVE/sieve_negative.csv -------------------------------------------------------------------------------- /tests/SIEVE/sieve_positive.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/tests/SIEVE/sieve_positive.csv -------------------------------------------------------------------------------- /tests/XCMS/params_amalgamator.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/tests/XCMS/params_amalgamator.json -------------------------------------------------------------------------------- /tests/XCMS/params_mssearch.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/tests/XCMS/params_mssearch.json -------------------------------------------------------------------------------- /tests/XCMS/params_peakfilter_negative.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/tests/XCMS/params_peakfilter_negative.json -------------------------------------------------------------------------------- /tests/XCMS/params_peakfilter_positive.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/tests/XCMS/params_peakfilter_positive.json -------------------------------------------------------------------------------- /tests/XCMS/xcms_negative.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/tests/XCMS/xcms_negative.csv -------------------------------------------------------------------------------- /tests/XCMS/xcms_positive.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ODonnell-Lipidomics/LipidFinder/HEAD/tests/XCMS/xcms_positive.csv --------------------------------------------------------------------------------