Index

A

aggregate() (in module pyXLMS.transform) (in module pyXLMS.transform.aggregate) AMINO_ACIDS (in module pyXLMS.constants)

AMINO_ACIDS_1TO3 (in module pyXLMS.constants) AMINO_ACIDS_3TO1 (in module pyXLMS.constants) assert_data_type_same() (in module pyXLMS.transform) (in module pyXLMS.transform.util)

C

check_indexing() (in module pyXLMS.data) check_input() (in module pyXLMS.data) check_input_multi() (in module pyXLMS.data) create_crosslink() (in module pyXLMS.data) create_crosslink_from_csm() (in module pyXLMS.data)

create_crosslink_min() (in module pyXLMS.data) create_csm() (in module pyXLMS.data) create_csm_min() (in module pyXLMS.data) create_parser_result() (in module pyXLMS.data) CROSSLINKERS (in module pyXLMS.constants)

D

detect_scout_filetype() (in module pyXLMS.parser) (in module pyXLMS.parser.parser_xldbse_scout)

detect_xi_filetype() (in module pyXLMS.parser) (in module pyXLMS.parser.parser_xldbse_xi)

F

fasta_title_to_accession() (in module pyXLMS.transform) (in module pyXLMS.transform.reannotate_positions) filter_crosslink_type() (in module pyXLMS.transform) (in module pyXLMS.transform.filter)

filter_proteins() (in module pyXLMS.transform) (in module pyXLMS.transform.filter) filter_target_decoy() (in module pyXLMS.transform) (in module pyXLMS.transform.filter) format_sequence() (in module pyXLMS.parser.util)

G

get_available_keys() (in module pyXLMS.transform) (in module pyXLMS.transform.util)

get_bool_from_value() (in module pyXLMS.parser.util) get_msannika_crosslink_sequence() (in module pyXLMS.exporter) (in module pyXLMS.exporter.to_msannika)

M

MODIFICATIONS (in module pyXLMS.constants) modifications_to_str() (in module pyXLMS.transform) (in module pyXLMS.transform.util) module pyXLMS pyXLMS.constants pyXLMS.data pyXLMS.exporter pyXLMS.exporter.to_impxfdr pyXLMS.exporter.to_msannika pyXLMS.exporter.to_pyxlinkviewer pyXLMS.exporter.to_xifdr pyXLMS.exporter.to_xinet pyXLMS.exporter.to_xiview pyXLMS.exporter.to_xlinkdb pyXLMS.exporter.to_xlmstools pyXLMS.exporter.to_xmas pyXLMS.exporter.util pyXLMS.parser pyXLMS.parser.parser_xldbse_custom pyXLMS.parser.parser_xldbse_maxquant pyXLMS.parser.parser_xldbse_msannika pyXLMS.parser.parser_xldbse_mzid pyXLMS.parser.parser_xldbse_plink pyXLMS.parser.parser_xldbse_scout pyXLMS.parser.parser_xldbse_xi pyXLMS.parser.parser_xldbse_xlinkx pyXLMS.parser.util pyXLMS.pipelines pyXLMS.plotting pyXLMS.plotting.plot_score_distribution pyXLMS.plotting.plot_venn_diagram pyXLMS.transform pyXLMS.transform.aggregate pyXLMS.transform.filter pyXLMS.transform.reannotate_positions pyXLMS.transform.summary pyXLMS.transform.targets_only pyXLMS.transform.to_dataframe pyXLMS.transform.to_proforma pyXLMS.transform.util pyXLMS.transform.validate

P

parse_modifications_from_maxquant_sequence() (in module pyXLMS.parser) (in module pyXLMS.parser.parser_xldbse_maxquant) parse_modifications_from_scout_sequence() (in module pyXLMS.parser) (in module pyXLMS.parser.parser_xldbse_scout) parse_modifications_from_xi_sequence() (in module pyXLMS.parser) (in module pyXLMS.parser.parser_xldbse_xi) parse_peptide() (in module pyXLMS.parser) (in module pyXLMS.parser.parser_xldbse_xi) parse_scan_nr_from_mzid() (in module pyXLMS.parser) (in module pyXLMS.parser.parser_xldbse_mzid) parse_scan_nr_from_plink() (in module pyXLMS.parser) (in module pyXLMS.parser.parser_xldbse_plink) parse_spectrum_file_from_plink() (in module pyXLMS.parser) (in module pyXLMS.parser.parser_xldbse_plink) pipeline() (in module pyXLMS.pipelines) plot_score_distribution() (in module pyXLMS.plotting) (in module pyXLMS.plotting.plot_score_distribution) plot_venn_diagram() (in module pyXLMS.plotting) (in module pyXLMS.plotting.plot_venn_diagram) pyXLMS module pyXLMS.constants module pyXLMS.data module pyXLMS.exporter module pyXLMS.exporter.to_impxfdr module pyXLMS.exporter.to_msannika module pyXLMS.exporter.to_pyxlinkviewer module pyXLMS.exporter.to_xifdr module pyXLMS.exporter.to_xinet module pyXLMS.exporter.to_xiview module pyXLMS.exporter.to_xlinkdb module pyXLMS.exporter.to_xlmstools module pyXLMS.exporter.to_xmas module pyXLMS.exporter.util module pyXLMS.parser module

pyXLMS.parser.parser_xldbse_custom module pyXLMS.parser.parser_xldbse_maxquant module pyXLMS.parser.parser_xldbse_msannika module pyXLMS.parser.parser_xldbse_mzid module pyXLMS.parser.parser_xldbse_plink module pyXLMS.parser.parser_xldbse_scout module pyXLMS.parser.parser_xldbse_xi module pyXLMS.parser.parser_xldbse_xlinkx module pyXLMS.parser.util module pyXLMS.pipelines module pyXLMS.plotting module pyXLMS.plotting.plot_score_distribution module pyXLMS.plotting.plot_venn_diagram module pyXLMS.transform module pyXLMS.transform.aggregate module pyXLMS.transform.filter module pyXLMS.transform.reannotate_positions module pyXLMS.transform.summary module pyXLMS.transform.targets_only module pyXLMS.transform.to_dataframe module pyXLMS.transform.to_proforma module pyXLMS.transform.util module pyXLMS.transform.validate module pyxlms_modification_str_parser() (in module pyXLMS.parser) (in module pyXLMS.parser.parser_xldbse_custom)

R

read() (in module pyXLMS.parser) read_custom() (in module pyXLMS.parser) (in module pyXLMS.parser.parser_xldbse_custom) read_maxlynx() (in module pyXLMS.parser) (in module pyXLMS.parser.parser_xldbse_maxquant) read_maxquant() (in module pyXLMS.parser) (in module pyXLMS.parser.parser_xldbse_maxquant) read_msannika() (in module pyXLMS.parser) (in module pyXLMS.parser.parser_xldbse_msannika) read_mzid() (in module pyXLMS.parser) (in module pyXLMS.parser.parser_xldbse_mzid)

read_plink() (in module pyXLMS.parser) (in module pyXLMS.parser.parser_xldbse_plink) read_scout() (in module pyXLMS.parser) (in module pyXLMS.parser.parser_xldbse_scout) read_xi() (in module pyXLMS.parser) (in module pyXLMS.parser.parser_xldbse_xi) read_xlinkx() (in module pyXLMS.parser) (in module pyXLMS.parser.parser_xldbse_xlinkx) reannotate_positions() (in module pyXLMS.transform) (in module pyXLMS.transform.reannotate_positions)

S

SCOUT_MODIFICATION_MAPPING (in module pyXLMS.constants)

summary() (in module pyXLMS.transform) (in module pyXLMS.transform.summary)

T

targets_only() (in module pyXLMS.transform) (in module pyXLMS.transform.targets_only) to_dataframe() (in module pyXLMS.transform) (in module pyXLMS.transform.to_dataframe) to_impxfdr() (in module pyXLMS.exporter) (in module pyXLMS.exporter.to_impxfdr) to_msannika() (in module pyXLMS.exporter) (in module pyXLMS.exporter.to_msannika) to_proforma() (in module pyXLMS.transform) (in module pyXLMS.transform.to_proforma) to_pyxlinkviewer() (in module pyXLMS.exporter) (in module pyXLMS.exporter.to_pyxlinkviewer)

to_xifdr() (in module pyXLMS.exporter) (in module pyXLMS.exporter.to_xifdr) to_xinet() (in module pyXLMS.exporter) (in module pyXLMS.exporter.to_xinet) to_xiview() (in module pyXLMS.exporter) (in module pyXLMS.exporter.to_xiview) to_xlinkdb() (in module pyXLMS.exporter) (in module pyXLMS.exporter.to_xlinkdb) to_xlmstools() (in module pyXLMS.exporter) (in module pyXLMS.exporter.to_xlmstools) to_xmas() (in module pyXLMS.exporter) (in module pyXLMS.exporter.to_xmas)

U

unique() (in module pyXLMS.transform) (in module pyXLMS.transform.aggregate)

V

validate() (in module pyXLMS.transform) (in module pyXLMS.transform.validate)

venn() (in module pyXLMS.plotting) (in module pyXLMS.plotting.plot_venn_diagram)

X

XI_MODIFICATION_MAPPING (in module pyXLMS.constants)