Index

_

__init__() (ms_mint.Chromatogram.Chromatogram method) (ms_mint.filelock.BaseFileLock method) (ms_mint.filelock.Timeout method) (ms_mint.filters.GaussFilter method) (ms_mint.filters.Resampler method) (ms_mint.filters.Smoother method) (ms_mint.pca.PCA_Plotter method) (ms_mint.pca.PrincipalComponentsAnalyser method)

_acquire() (ms_mint.filelock.BaseFileLock method) _release() (ms_mint.filelock.BaseFileLock method) _scale_group() (ms_mint.Mint.Mint method)

A

acquire() (ms_mint.filelock.BaseFileLock method)

append_results() (in module ms_mint.processing) apply_filters() (ms_mint.Chromatogram.Chromatogram method)

B

BaseFileLock (class in ms_mint.filelock)

C

check_targets() (in module ms_mint.targets) Chromatogram (class in ms_mint.Chromatogram) clear_ms_files() (ms_mint.Mint.Mint method) clear_results() (ms_mint.Mint.Mint method) clear_targets() (ms_mint.Mint.Mint method) convert_ms_file_to_feather() (in module ms_mint.io)

convert_ms_file_to_parquet() (in module ms_mint.io) convert_to_seconds() (in module ms_mint.targets) crosstab() (ms_mint.Mint.Mint method) cumulative_variance() (ms_mint.pca.PCA_Plotter method) cumulative_variance_px() (ms_mint.pca.PCA_Plotter method) cumulative_variance_sns() (ms_mint.pca.PCA_Plotter method)

D

data (ms_mint.Chromatogram.Chromatogram property) df_diff() (in module ms_mint.tools) df_to_numeric() (in module ms_mint.io)

diff_targets() (in module ms_mint.targets) digest_results() (ms_mint.Mint.Mint method) display() (ms_mint.notebook.Mint method)

E

estimate_noise_level() (ms_mint.Chromatogram.Chromatogram method) export() (ms_mint.Mint.Mint method)

export_to_excel() (in module ms_mint.io) extract_chromatogram_from_ms1() (in module ms_mint.processing) extract_ms1_properties() (in module ms_mint.processing)

F

FileLock (in module ms_mint.filelock) fill_missing_rt_values() (in module ms_mint.targets) Filter (class in ms_mint.filters) find_peaks() (ms_mint.Chromatogram.Chromatogram method)

find_peaks_in_timeseries() (in module ms_mint.tools) fn_to_label() (in module ms_mint.tools) format_thermo_raw_file_reader_parquet() (in module ms_mint.io) formula_to_mass() (in module ms_mint.tools) from_file() (ms_mint.Chromatogram.Chromatogram method)

G

GaussFilter (class in ms_mint.filters) gaussian() (in module ms_mint.tools) gen_target_grid() (in module ms_mint.targets) get_chromatogram_from_ms_file() (in module ms_mint.processing)

get_chromatograms() (ms_mint.Mint.Mint method) get_ms_files_from_results() (in module ms_mint.tools) get_palette_colors() (in module ms_mint.plotly_tools) get_target_params() (ms_mint.Mint.Mint method) get_targets_from_results() (in module ms_mint.tools)

H

hierarchical_clustering() (in module ms_mint.matplotlib_tools)

I

init_metadata() (in module ms_mint.tools)

is_locked (ms_mint.filelock.BaseFileLock property) is_ms_file() (in module ms_mint.tools)

L

load() (ms_mint.Mint.Mint method) load_files() (ms_mint.Mint.Mint method) load_metadata() (ms_mint.Mint.Mint method) load_targets() (ms_mint.Mint.Mint method) loadings() (ms_mint.pca.PCA_Plotter method)

loadings_plotly() (ms_mint.pca.PCA_Plotter method) loadings_sns() (ms_mint.pca.PCA_Plotter method) lock() (in module ms_mint.tools) lock_file (ms_mint.filelock.BaseFileLock property) (ms_mint.filelock.Timeout attribute) log2p1() (in module ms_mint.tools)

M

messages (ms_mint.notebook.Mint property) Mint (class in ms_mint.Mint) (class in ms_mint.notebook) module ms_mint ms_mint.Chromatogram ms_mint.filelock ms_mint.filters ms_mint.io ms_mint.matplotlib_tools ms_mint.Mint ms_mint.notebook ms_mint.pca ms_mint.plotly_tools ms_mint.processing ms_mint.standards ms_mint.targets ms_mint.tools ms_file_to_df() (in module ms_mint.io) ms_files (ms_mint.Mint.Mint property) ms_mint module ms_mint.Chromatogram module ms_mint.filelock module

ms_mint.filters module ms_mint.io module ms_mint.matplotlib_tools module ms_mint.Mint module ms_mint.notebook module ms_mint.pca module ms_mint.plotly_tools module ms_mint.processing module ms_mint.standards module ms_mint.targets module ms_mint.tools module mz_mean_width_to_min_max() (in module ms_mint.tools) mzml_to_df() (in module ms_mint.io) mzml_to_pandas_df_pyteomics() (in module ms_mint.io) mzmlb_to_df__pyteomics() (in module ms_mint.io) mzxml_to_df() (in module ms_mint.io)

N

n_files (ms_mint.Mint.Mint property)

O

optimise_peak_times_with_diff() (ms_mint.Chromatogram.Chromatogram method)

P

pairplot() (ms_mint.pca.PCA_Plotter method) pairplot_plotly() (ms_mint.pca.PCA_Plotter method) pairplot_sns() (ms_mint.pca.PCA_Plotter method) PCA_Plotter (class in ms_mint.pca) peak_labels (ms_mint.Mint.Mint property) plot() (ms_mint.Chromatogram.Chromatogram method) plot_metabolomics_hist2d() (in module ms_mint.matplotlib_tools) plot_peak_shapes() (in module ms_mint.matplotlib_tools)

plot_peaks() (in module ms_mint.matplotlib_tools) plotly_heatmap() (in module ms_mint.plotly_tools) plotly_peak_shapes() (in module ms_mint.plotly_tools) PrincipalComponentsAnalyser (class in ms_mint.pca) process_ms1() (in module ms_mint.processing) process_ms1_file() (in module ms_mint.processing) process_ms1_files_in_parallel() (in module ms_mint.processing) process_ms1_from_numpy() (in module ms_mint.processing) progress (ms_mint.Mint.Mint property)

R

read_parquet() (in module ms_mint.io) read_targets() (in module ms_mint.targets) release() (ms_mint.filelock.BaseFileLock method) Resampler (class in ms_mint.filters)

reset() (ms_mint.Mint.Mint method) results (ms_mint.Mint.Mint property) run() (ms_mint.Mint.Mint method) (ms_mint.pca.PrincipalComponentsAnalyser method)

S

save_metadata() (ms_mint.Mint.Mint method) scale_dataframe() (in module ms_mint.tools) score_peaks() (in module ms_mint.processing) select_peak_by_highest_intensity() (ms_mint.Chromatogram.Chromatogram method) select_peak_by_rt() (ms_mint.Chromatogram.Chromatogram method) select_peak_with_gaussian_weight() (ms_mint.Chromatogram.Chromatogram method) selected_peaks (ms_mint.Chromatogram.Chromatogram property)

set_dtypes() (in module ms_mint.io) set_template() (in module ms_mint.plotly_tools) slice_ms1_array() (in module ms_mint.processing) Smoother (class in ms_mint.filters) SoftFileLock (class in ms_mint.filelock) standardize_targets() (in module ms_mint.targets) status (ms_mint.Mint.Mint property)

T

targets (ms_mint.Mint.Mint property) Timeout timeout (ms_mint.filelock.BaseFileLock property)

transform() (ms_mint.filters.Filter method) (ms_mint.filters.GaussFilter method) (ms_mint.filters.Resampler method) (ms_mint.filters.Smoother method)

U

UnixFileLock (class in ms_mint.filelock)

V

version (ms_mint.Mint.Mint attribute)

W

WindowsFileLock (class in ms_mint.filelock)