Index

A

Affinity (class in msdas.clustering) AffinityPropagation() (Affinity method) AND (MassSpecAlignmentBase attribute) (MassSpecReader attribute) (PSites attribute) annotations (Annotations attribute)

Annotations (class in msdas.annotations) AnnotationsYeast (class in msdas.annotations) append_oxidation() (PSites method) average() (Replicates method)

B

boxplot() (MassSpecReader method) boxplot_errors() (YEAST2MIDAS method)

boxplot_replicates_by_experiment() (Replicates method) build_mapping_from_df() (Annotations method)

C

check_entries_versus_sequence() (Annotations method) check_format() (MassSpecAlignmentBase method) clean_na_paper() (ReplicatesYeast method) clean_na_paper2() (ReplicatesYeast method) Cleaner (class in msdas.readers) cleanup() (MassSpecReader method)

cleanup_june() (YEAST2MIDAS method) cluster_centers_indices (Affinity attribute) CombineNetworks (class in msdas.network) copy() (Replicates method) (ReplicatesYeast method) corr2d() (YEAST2MIDAS method) corr2d_all() (YEAST2MIDAS method)

D

dendogram() (MSClustering method) df (MassSpecAlignmentBase attribute) (MassSpecReader attribute) drop_na_count() (Cleaner method)

drop_na_exceeds_minnonzero() (ReplicatesYeast method) drop_oxidation() (Cleaner method)

E

example (Modification attribute) export2sif() (PhosphoGRID method)

export_pkn_and_midas() (YEAST2MIDAS method) export_pkn_and_midas_june() (YEAST2MIDAS method)

F

find_sequence_blast() (Annotations method)

fix_duplicated_identifier() (Cleaner method)

G

get_average_mu() (Replicates method) get_average_sigma() (Replicates method) get_cnograph_intact() (NetworkFromUniProt method) get_coefficient_variation() (Replicates method) (YEAST2MIDAS method) get_coefficient_variation_df() (Replicates method) get_common_psites() (PSites method) get_cv() (YEAST2MIDAS method) get_data_matrix() (MassSpecReader method) get_df_exemplars() (YEAST2MIDAS method) get_digraph() (CombineNetworks method) get_errors() (Replicates method) (YEAST2MIDAS method) get_expanded_cnograph() (YEAST2MIDAS method) get_factorised_psites() (PSites method) get_group() (MSClustering method) get_group_psite() (YEAST2MIDAS method) get_group_psite_transposed() (YEAST2MIDAS method) get_individual_psites() (Modification method) get_mean_errors_df() (Replicates method) get_midas() (YEAST2MIDAS method) get_mu_df() (Replicates method)

get_multiedge_graph() (CombineNetworks method) get_mus() (Replicates method) get_na_count() (Cleaner method) get_na_per_experiment_after_averaging() (ReplicatesYeast method) get_na_per_salt_experiment_after_averaging() (ReplicatesYeast method) get_protein_from_fasta_header() (SequenceTools method) get_proteinId_from_fasta_header() (SequenceTools method) get_psites_exemplars() (YEAST2MIDAS method) get_psites_mapping() (YEAST2MIDAS method) get_replicates_from_one_unique_measurement() (Replicates method) get_sigmas() (Replicates method) get_standarised_residuals() (Replicates method) get_uniprot_entries() (Annotations method) get_unique_measurement_name() (Replicates method) get_unique_psites() (PSites method) get_yeast_filenames() (in module msdas.yeast) get_yeast_raw_data() (in module msdas.yeast) get_yeast_small_data() (in module msdas.yeast) groups (MSClustering attribute) (YEAST2MIDAS attribute) groups_cluster() (YEAST2MIDAS method)

H

header_mapping (MassSpecReader attribute) hist2d_errors_versus_cv() (Replicates method) hist2d_mu_versus_cv() (Replicates method) hist_coefficient_variation() (Replicates method)

hist_most_relevant_goids() (Annotations method) hist_na_per_experiments() (Replicates method) hist_number_peptides() (MassSpecReader method) hist_peptide_sequence_length() (MassSpecReader method)

I

interpolate_time0() (YEAST2MIDAS method) is_na_count_exceeds_minnonzero_in_all_experiment() (ReplicatesYeast method)

isvalid() (PSites method)

L

labels (Affinity attribute) location

log_b2() (ReplicatesYeast method)

M

mapping_small_to_raw_june() (YEAST2MIDAS method) MassSpecAlignmentBase (class in msdas.alignment) MassSpecAlignmentYeast (class in msdas.alignment) MassSpecReader (class in msdas.readers) measurements (MassSpecReader attribute) merge() (MassSpecAlignmentBase method) merge_identical_peptide_sequence() (Cleaner method) merge_on (MassSpecAlignmentBase attribute) merge_peptides() (MassSpecReader method) merge_peptides_with_same_psites() (Cleaner method) metadata (MassSpecReader attribute) mode (MassSpecAlignmentBase attribute) (MassSpecReader attribute) modif2psites() (Modification method)

Modification (class in msdas.tools) modification (Modification attribute) MSClustering (class in msdas.clustering) msdas.alignment (module) msdas.annotations (module) msdas.clustering (module) msdas.network (module) msdas.phosphogrid (module) msdas.psites (module) msdas.readers (module) msdas.replicates (module) msdas.tools (module) msdas.yeast (module)

N

N (MassSpecReader attribute) nclusters (Affinity attribute)

NetworkFromUniProt (class in msdas.network) normalise() (ReplicatesYeast method)

O

OR (MassSpecReader attribute) (PSites attribute)

P

pcolor() (MassSpecReader method) pcolor_errors() (YEAST2MIDAS method) pcolor_na() (Replicates method) (YEAST2MIDAS method) PhosphoGRID (class in msdas.phosphogrid) phosphorylation plot() (PhosphoGRID method) plot_experiments() (MassSpecReader method) plot_figure6() (YEAST2MIDAS method) plot_goid_histogram() (Annotations method) plot_group() (YEAST2MIDAS method) plot_mu_sigma() (Replicates method) plot_multiedge_graph() (CombineNetworks method) plot_na_per_experiment() (Replicates method)

plot_phospho_stats() (MassSpecReader method) plot_psites_mapping() (YEAST2MIDAS method) plot_timeseries() (MassSpecReader method) plot_timeseries_midas() (ReplicatesYeast method) (YEAST2MIDAS method) plot_vectors() (MSClustering method) plotClusteredProtein() (MSClustering method) plotClusters() (Affinity method) (MSClustering method) plotClusters_and_protein() (Affinity method) (MSClustering method) preference (Affinity attribute) psite PSites (class in msdas.psites) psites (MassSpecReader attribute) (Modification attribute) psites2modif() (Modification method)

R

read_annotations() (MassSpecReader method) read_csv() (MassSpecReader method) read_pickle() (Annotations method) remove_ambiguities() (MassSpecReader method) remove_ambiguous_proteins() (MassSpecReader method) remove_ambiguous_psites() (MassSpecReader method) remove_duplicated() (PSites method) remove_protein() (YEAST2MIDAS method) remove_spaces() (PSites method)

remove_species_not_in_pkn() (YEAST2MIDAS method) rename_psites() (MassSpecReader method) replicates Replicates (class in msdas.replicates) ReplicatesYeast (class in msdas.replicates) Requires (class in msdas.tools) reset() (Replicates method) run() (PhosphoGRID method) run_affinity_propagation_clustering() (MSClustering method)

S

scale() (MSClustering method) (ReplicatesYeast method) sequence sequences (MassSpecReader attribute) SequenceTools (class in msdas.tools) set_annotations() (Annotations method) set_irrelevant_replicates_to_na() (Replicates method)

set_zero_to_na() (Cleaner method) show_sequence() (MassSpecReader method) sort_psites_ors_only() (MassSpecReader method) (PSites method) sorted() (PSites method) status() (MassSpecReader method)

T

times (ReplicatesYeast attribute) (YEAST attribute) to_csv() (Annotations method) (MassSpecReader method)

to_midas() (YEAST2MIDAS method) to_pickle() (Annotations method)

U

update_mapping() (AnnotationsYeast method)

V

valid_header (MassSpecReader attribute)

X

xmidas_errors() (YEAST2MIDAS method)

Y

YEAST (class in msdas.yeast) YEAST2MIDAS (class in msdas.yeast)

yeast_tags (ReplicatesYeast attribute)