DIMSPy
0.1
Contents:
Introduction
dimspy package
DIMSPy
Docs
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Index
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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L
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M
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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
A
add_attribute() (dimspy.models.peaklist.PeakList method)
add_flag() (dimspy.models.peak_matrix.PeakMatrix method)
add_tags() (dimspy.models.peaklist_tags.PeakList_Tags method)
align_peaks() (in module dimspy.process.peak_alignment)
align_samples() (in module dimspy.workflow)
attr_matrix() (dimspy.models.peak_matrix.PeakMatrix method)
attr_mean_vector() (dimspy.models.peak_matrix.PeakMatrix method)
attributes (dimspy.models.peak_matrix.PeakMatrix attribute)
(dimspy.models.peaklist.PeakList attribute)
average_replicate_scans() (in module dimspy.process.scan_processing)
B
blank_filter() (in module dimspy.workflow)
C
calculate_flags() (dimspy.models.peaklist.PeakList method)
check_metadata() (in module dimspy.experiment)
check_paths() (in module dimspy.portals.paths)
cleanup_unflagged_peaks() (dimspy.models.peaklist.PeakList method)
close() (dimspy.portals.thermo_raw_portal.ThermoRaw method)
copy() (dimspy.models.peaklist.PeakList method)
count_ms_types() (in module dimspy.experiment)
count_scan_types() (in module dimspy.experiment)
D
dimspy (module)
dimspy.dimspy (module)
dimspy.experiment (module)
dimspy.log_setting (module)
dimspy.models (module)
dimspy.models.peak_matrix (module)
dimspy.models.peaklist (module)
dimspy.models.peaklist_metadata (module)
dimspy.models.peaklist_tags (module)
dimspy.portals (module)
dimspy.portals.hdf5_portal (module)
dimspy.portals.mzml_portal (module)
dimspy.portals.paths (module)
dimspy.portals.thermo_raw_portal (module)
dimspy.portals.txt_portal (module)
dimspy.process (module)
dimspy.process.mass_calibration (module)
dimspy.process.peak_alignment (module)
dimspy.process.peak_filters (module)
dimspy.process.scan_processing (module)
dimspy.workflow (module)
drop_all_tags() (dimspy.models.peaklist_tags.PeakList_Tags method)
drop_attribute() (dimspy.models.peaklist.PeakList method)
drop_flag() (dimspy.models.peak_matrix.PeakMatrix method)
drop_tag_types() (dimspy.models.peaklist_tags.PeakList_Tags method)
drop_tags() (dimspy.models.peaklist_tags.PeakList_Tags method)
dtable (dimspy.models.peaklist.PeakList attribute)
E
extra_info() (dimspy.portals.mzml_portal.Mzml method)
extract_peaklist() (dimspy.models.peak_matrix.PeakMatrix method)
extract_peaklists() (dimspy.models.peak_matrix.PeakMatrix method)
F
filter_attr() (in module dimspy.process.peak_filters)
filter_blank_peaks() (in module dimspy.process.peak_filters)
filter_fraction() (in module dimspy.process.peak_filters)
filter_mz_ranges() (in module dimspy.process.peak_filters)
filter_ringing() (in module dimspy.process.peak_filters)
filter_rsd() (in module dimspy.process.peak_filters)
flag_attributes (dimspy.models.peaklist.PeakList attribute)
flag_names (dimspy.models.peak_matrix.PeakMatrix attribute)
flag_values() (dimspy.models.peak_matrix.PeakMatrix method)
flags (dimspy.models.peak_matrix.PeakMatrix attribute)
(dimspy.models.peaklist.PeakList attribute)
format() (dimspy.log_setting.LevelFormatter method)
fraction (dimspy.models.peak_matrix.PeakMatrix attribute)
full_shape (dimspy.models.peak_matrix.PeakMatrix attribute)
(dimspy.models.peaklist.PeakList attribute)
full_size (dimspy.models.peaklist.PeakList attribute)
G
get_attribute() (dimspy.models.peaklist.PeakList method)
get_peak() (dimspy.models.peaklist.PeakList method)
H
has_attribute() (dimspy.models.peaklist.PeakList method)
has_tag() (dimspy.models.peaklist_tags.PeakList_Tags method)
has_tag_type() (dimspy.models.peaklist_tags.PeakList_Tags method)
hdf5_to_txt() (in module dimspy.workflow)
headers() (dimspy.portals.mzml_portal.Mzml method)
(dimspy.portals.thermo_raw_portal.ThermoRaw method)
headers_scan_ids() (dimspy.portals.mzml_portal.Mzml method)
(dimspy.portals.thermo_raw_portal.ThermoRaw method)
I
ID (dimspy.models.peaklist.PeakList attribute)
idxs_reps_from_filelist() (in module dimspy.experiment)
insert_peak() (dimspy.models.peaklist.PeakList method)
intensity_matrix (dimspy.models.peak_matrix.PeakMatrix attribute)
intensity_mean_vector (dimspy.models.peak_matrix.PeakMatrix attribute)
interpret_experiment() (in module dimspy.experiment)
is_empty() (dimspy.models.peak_matrix.PeakMatrix method)
J
join_peaklists() (in module dimspy.process.scan_processing)
L
LevelFormatter (class in dimspy.log_setting)
load_peak_matrix_from_hdf5() (in module dimspy.portals.hdf5_portal)
load_peak_matrix_from_txt() (in module dimspy.portals.txt_portal)
load_peaklist_from_txt() (in module dimspy.portals.txt_portal)
load_peaklists() (in module dimspy.workflow)
load_peaklists_from_hdf5() (in module dimspy.portals.hdf5_portal)
M
main() (in module dimspy.dimspy)
mask (dimspy.models.peak_matrix.PeakMatrix attribute)
mask_all_peakmatrix (class in dimspy.models.peak_matrix)
mask_peakmatrix (class in dimspy.models.peak_matrix)
mask_tags() (dimspy.models.peak_matrix.PeakMatrix method)
merge_peaklists() (in module dimspy.workflow)
metadata (dimspy.models.peaklist.PeakList attribute)
missing_values (dimspy.models.peak_matrix.PeakMatrix attribute)
mode_type_from_header() (in module dimspy.experiment)
ms_type_from_header() (in module dimspy.experiment)
mz_matrix (dimspy.models.peak_matrix.PeakMatrix attribute)
mz_mean_vector (dimspy.models.peak_matrix.PeakMatrix attribute)
mz_range_from_header() (in module dimspy.experiment)
(in module dimspy.portals.thermo_raw_portal)
Mzml (class in dimspy.portals.mzml_portal)
O
occurrence (dimspy.models.peak_matrix.PeakMatrix attribute)
P
peak_matrix_rsd() (in module dimspy.models.peak_matrix)
PeakList (class in dimspy.models.peaklist)
peaklist() (dimspy.portals.mzml_portal.Mzml method)
(dimspy.portals.thermo_raw_portal.ThermoRaw method)
peaklist_ids (dimspy.models.peak_matrix.PeakMatrix attribute)
PeakList_Metadata (class in dimspy.models.peaklist_metadata)
peaklist_tag_types (dimspy.models.peak_matrix.PeakMatrix attribute)
peaklist_tag_values (dimspy.models.peak_matrix.PeakMatrix attribute)
PeakList_Tags (class in dimspy.models.peaklist_tags)
peaklist_tags (dimspy.models.peak_matrix.PeakMatrix attribute)
peaklists() (dimspy.portals.mzml_portal.Mzml method)
(dimspy.portals.thermo_raw_portal.ThermoRaw method)
PeakMatrix (class in dimspy.models.peak_matrix)
peaks (dimspy.models.peaklist.PeakList attribute)
present (dimspy.models.peak_matrix.PeakMatrix attribute)
present_matrix (dimspy.models.peak_matrix.PeakMatrix attribute)
process_scans() (in module dimspy.workflow)
property() (dimspy.models.peak_matrix.PeakMatrix method)
purity (dimspy.models.peak_matrix.PeakMatrix attribute)
R
read_scans() (in module dimspy.process.scan_processing)
remove_edges() (in module dimspy.process.scan_processing)
remove_peak() (dimspy.models.peaklist.PeakList method)
remove_peaks() (dimspy.models.peak_matrix.PeakMatrix method)
remove_samples() (dimspy.models.peak_matrix.PeakMatrix method)
replicate_filter() (in module dimspy.workflow)
run() (dimspy.portals.mzml_portal.Mzml method)
S
sample_filter() (in module dimspy.workflow)
save_peak_matrix_as_hdf5() (in module dimspy.portals.hdf5_portal)
save_peak_matrix_as_txt() (in module dimspy.portals.txt_portal)
save_peaklist_as_txt() (in module dimspy.portals.txt_portal)
save_peaklists_as_hdf5() (in module dimspy.portals.hdf5_portal)
scan_type_from_header() (in module dimspy.experiment)
set_attribute() (dimspy.models.peaklist.PeakList method)
set_logging() (in module dimspy.log_setting)
set_peak() (dimspy.models.peaklist.PeakList method)
shape (dimspy.models.peak_matrix.PeakMatrix attribute)
(dimspy.models.peaklist.PeakList attribute)
size (dimspy.models.peaklist.PeakList attribute)
sort_peaks_order() (dimspy.models.peaklist.PeakList method)
stitch() (in module dimspy.workflow)
T
tag_of() (dimspy.models.peaklist_tags.PeakList_Tags method)
tag_types (dimspy.models.peaklist_tags.PeakList_Tags attribute)
tag_values (dimspy.models.peaklist_tags.PeakList_Tags attribute)
tags (dimspy.models.peaklist.PeakList attribute)
tags_of() (dimspy.models.peak_matrix.PeakMatrix method)
ThermoRaw (class in dimspy.portals.thermo_raw_portal)
tics() (dimspy.portals.mzml_portal.Mzml method)
to_dict() (dimspy.models.peaklist.PeakList method)
to_list() (dimspy.models.peaklist.PeakList method)
(dimspy.models.peaklist_tags.PeakList_Tags method)
to_peaklist() (dimspy.models.peak_matrix.PeakMatrix method)
to_str() (dimspy.models.peak_matrix.PeakMatrix method)
(dimspy.models.peaklist.PeakList method)
(dimspy.models.peaklist_tags.PeakList_Tags method)
typed_tags (dimspy.models.peaklist_tags.PeakList_Tags attribute)
U
unmask_all_peakmatrix (class in dimspy.models.peak_matrix)
unmask_peakmatrix (class in dimspy.models.peak_matrix)
unmask_tags() (dimspy.models.peak_matrix.PeakMatrix method)
untyped_tags (dimspy.models.peaklist_tags.PeakList_Tags attribute)
update_class_labels() (in module dimspy.experiment)
update_metadata() (in module dimspy.experiment)