ms2pip
v4.0.0-dev9
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Installation
Usage
Prediction models
Command line interface
Command line interface
Python API reference
ms2pip
ms2pip.constants
ms2pip.correlation
ms2pip.exceptions
ms2pip.result
ms2pip.spectrum
ms2pip.spectrum_input
ms2pip.spectrum_output
ms2pip
Index
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Index
Symbols
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A
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C
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D
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G
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I
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L
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M
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N
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O
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P
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R
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S
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T
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U
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W
Symbols
--add-retention-time
ms2pip-correlate command line option
ms2pip-predict-batch command line option
--compute-correlations
ms2pip-correlate command line option
--logging-level
ms2pip command line option
--model
ms2pip-annotate-spectra command line option
ms2pip-correlate command line option
ms2pip-get-training-data command line option
ms2pip-predict-batch command line option
ms2pip-predict-single command line option
--model-dir
ms2pip-correlate command line option
ms2pip-predict-batch command line option
ms2pip-predict-single command line option
--ms2-tolerance
ms2pip-annotate-spectra command line option
ms2pip-correlate command line option
ms2pip-get-training-data command line option
--output-format
ms2pip-predict-batch command line option
--output-name
ms2pip-annotate-spectra command line option
ms2pip-correlate command line option
ms2pip-get-training-data command line option
ms2pip-predict-batch command line option
ms2pip-predict-single command line option
--plot
ms2pip-predict-single command line option
--processes
ms2pip-annotate-spectra command line option
ms2pip-correlate command line option
ms2pip-get-training-data command line option
ms2pip-predict-batch command line option
--psm-filetype
ms2pip-annotate-spectra command line option
ms2pip-correlate command line option
ms2pip-get-training-data command line option
--spectrum-id-pattern
ms2pip-annotate-spectra command line option
ms2pip-correlate command line option
ms2pip-get-training-data command line option
--version
ms2pip command line option
-f
ms2pip-predict-batch command line option
-l
ms2pip command line option
-n
ms2pip-annotate-spectra command line option
ms2pip-correlate command line option
ms2pip-get-training-data command line option
ms2pip-predict-batch command line option
-o
ms2pip-annotate-spectra command line option
ms2pip-correlate command line option
ms2pip-get-training-data command line option
ms2pip-predict-batch command line option
ms2pip-predict-single command line option
-p
ms2pip-annotate-spectra command line option
ms2pip-correlate command line option
ms2pip-get-training-data command line option
ms2pip-predict-single command line option
-r
ms2pip-correlate command line option
ms2pip-predict-batch command line option
-t
ms2pip-annotate-spectra command line option
ms2pip-correlate command line option
ms2pip-get-training-data command line option
-x
ms2pip-correlate command line option
A
annotate_spectra() (in module ms2pip)
as_spectra() (ms2pip.result.ProcessingResult method)
C
calculate_correlations() (in module ms2pip.result)
clip_intensity() (ms2pip.spectrum.Spectrum method)
correlate() (in module ms2pip)
correlations_to_csv() (in module ms2pip.result)
D
download_models() (in module ms2pip)
G
get_normalized_predictions() (ms2pip.spectrum_output.SpectrumOutput method)
get_training_data() (in module ms2pip)
I
InvalidAminoAcidError
InvalidInputError
InvalidPeptidoformError
InvalidWriteModeError
InvalidXGBoostModelError
L
log2_transform() (ms2pip.spectrum.Spectrum method)
M
module
ms2pip
ms2pip.correlation
ms2pip.exceptions
ms2pip.result
ms2pip.spectrum
ms2pip.spectrum_input
ms2pip.spectrum_output
ms2pip
module
ms2pip command line option
--logging-level
--version
-l
ms2pip-annotate-spectra command line option
--model
--ms2-tolerance
--output-name
--processes
--psm-filetype
--spectrum-id-pattern
-n
-o
-p
-t
PSMS
SPECTRUM_FILE
ms2pip-correlate command line option
--add-retention-time
--compute-correlations
--model
--model-dir
--ms2-tolerance
--output-name
--processes
--psm-filetype
--spectrum-id-pattern
-n
-o
-p
-r
-t
-x
PSMS
SPECTRUM_FILE
ms2pip-get-training-data command line option
--model
--ms2-tolerance
--output-name
--processes
--psm-filetype
--spectrum-id-pattern
-n
-o
-p
-t
PSMS
SPECTRUM_FILE
ms2pip-predict-batch command line option
--add-retention-time
--model
--model-dir
--output-format
--output-name
--processes
-f
-n
-o
-r
PSMS
ms2pip-predict-single command line option
--model
--model-dir
--output-name
--plot
-o
-p
PEPTIDOFORM
ms2pip.constants.MODELS (built-in variable)
ms2pip.constants.SUPPORTED_OUTPUT_FORMATS (built-in variable)
ms2pip.correlation
module
ms2pip.exceptions
module
ms2pip.result
module
ms2pip.spectrum
module
ms2pip.spectrum_input
module
ms2pip.spectrum_output
module
ms2pip_pearson() (in module ms2pip.correlation)
MS2PIPError
N
NoMatchingSpectraFound
O
ObservedSpectrum (class in ms2pip.spectrum)
P
PEPTIDOFORM
ms2pip-predict-single command line option
plot_spectra() (ms2pip.result.ProcessingResult method)
predict_batch() (in module ms2pip)
predict_library() (in module ms2pip)
predict_single() (in module ms2pip)
PredictedSpectrum (class in ms2pip.spectrum)
ProcessingResult (class in ms2pip.result)
PSMS
ms2pip-annotate-spectra command line option
ms2pip-correlate command line option
ms2pip-get-training-data command line option
ms2pip-predict-batch command line option
R
read_mgf() (in module ms2pip.spectrum_input)
read_mzml() (in module ms2pip.spectrum_input)
read_spectrum_file() (in module ms2pip.spectrum_input)
read_tdf() (in module ms2pip.spectrum_input)
remove_precursor() (ms2pip.spectrum.Spectrum method)
remove_reporter_ions() (ms2pip.spectrum.Spectrum method)
results_to_csv() (in module ms2pip.result)
S
spectral_angle() (in module ms2pip.correlation)
Spectrum (class in ms2pip.spectrum)
SPECTRUM_FILE
ms2pip-annotate-spectra command line option
ms2pip-correlate command line option
ms2pip-get-training-data command line option
SpectrumOutput (class in ms2pip.spectrum_output)
T
tic (ms2pip.spectrum.Spectrum property)
tic_norm() (ms2pip.spectrum.Spectrum method)
TitlePatternError
to_spectrum_utils() (ms2pip.spectrum.Spectrum method)
U
UnknownModelError
UnknownOutputFormatError
UnresolvableModificationError
UnsupportedSpectrumFiletypeError
W
write_bibliospec() (ms2pip.spectrum_output.SpectrumOutput method)
write_csv() (ms2pip.spectrum_output.SpectrumOutput method)
write_dlib() (ms2pip.spectrum_output.SpectrumOutput method)
write_mgf() (ms2pip.spectrum_output.SpectrumOutput method)
write_msp() (ms2pip.spectrum_output.SpectrumOutput method)
write_results() (ms2pip.spectrum_output.SpectrumOutput method)
write_single_spectrum_csv() (in module ms2pip.spectrum_output)
write_single_spectrum_png() (in module ms2pip.spectrum_output)
write_spectronaut() (ms2pip.spectrum_output.SpectrumOutput method)
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v: v4.0.0-dev9
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