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pyproteome version documentation
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T
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U
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V
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W
A
abs_pos (pyproteome.data_sets.Modification attribute)
(pyproteome.data_sets.modification.Modification attribute)
accessions (pyproteome.data_sets.data_set.DataSet attribute)
(pyproteome.data_sets.DataSet attribute)
(pyproteome.data_sets.Proteins attribute)
(pyproteome.data_sets.protein.Proteins attribute)
add_peptide() (pyproteome.data_sets.data_set.DataSet method)
(pyproteome.data_sets.DataSet method)
adjust_text() (in module pyproteome.utils)
allowed_mod_type() (in module pyproteome.data_sets.modification)
auto_clusterer() (in module pyproteome.cluster.auto)
B
BASE_DIR (in module pyproteome.paths)
C
calculate_es_s() (in module pyproteome.pathways.enrichments)
calculate_es_s_ud() (in module pyproteome.pathways.enrichments)
CAMV_NAME (in module pyproteome.paths)
CAMV_OUT_DIR (in module pyproteome.paths)
cdf() (pyproteome.pathways.enrichments.PrPDF method)
changes_table() (in module pyproteome.analysis.tables)
char_mapping (pyproteome.motifs.motif.Motif attribute)
check_raw() (pyproteome.data_sets.data_set.DataSet method)
(pyproteome.data_sets.DataSet method)
children() (pyproteome.motifs.motif.Motif method)
cluster() (in module pyproteome.cluster.clusterer)
cluster_corrmap() (in module pyproteome.cluster.plot)
cluster_range() (in module pyproteome.cluster.plot)
constand() (in module pyproteome.data_sets.constand)
CONSTAND_METHODS (in module pyproteome.data_sets.constand)
copy() (pyproteome.data_sets.data_set.DataSet method)
(pyproteome.data_sets.DataSet method)
(pyproteome.data_sets.Modification method)
(pyproteome.data_sets.Modifications method)
(pyproteome.data_sets.modification.Modification method)
(pyproteome.data_sets.modification.Modifications method)
(pyproteome.utils.DefaultOrderedDict method)
correlate_data_sets() (in module pyproteome.analysis.correlation)
correlate_phenotype() (in module pyproteome.pathways.enrichments)
correlate_signal() (in module pyproteome.analysis.correlation)
CORRELATION_METRICS (in module pyproteome.pathways.enrichments)
D
data (pyproteome.data_sets.data_set.DataSet attribute)
(pyproteome.data_sets.DataSet attribute)
DATA_SET_COLS (in module pyproteome.data_sets.data_set)
DataSet (class in pyproteome.data_sets)
(class in pyproteome.data_sets.data_set)
DEFAULT_CORR_CPUS (in module pyproteome.pathways.enrichments)
DEFAULT_DPI (in module pyproteome.utils)
DEFAULT_FILTER_BAD (in module pyproteome.data_sets.data_set)
DEFAULT_RANK_CPUS (in module pyproteome.pathways.enrichments)
DefaultOrderedDict (class in pyproteome.utils)
descriptions (pyproteome.data_sets.protein.Proteins attribute)
(pyproteome.data_sets.Proteins attribute)
display_mod_type() (pyproteome.data_sets.Modification method)
(pyproteome.data_sets.modification.Modification method)
draw_protein_seq() (in module pyproteome.analysis.protein)
dropna() (pyproteome.data_sets.data_set.DataSet method)
(pyproteome.data_sets.DataSet method)
E
enriched_neighborhood() (in module pyproteome.motifs.neighborhood)
enrichment_scores() (in module pyproteome.pathways.enrichments)
estimate_pq() (in module pyproteome.pathways.enrichments)
exact (pyproteome.data_sets.Modification attribute)
(pyproteome.data_sets.modification.Modification attribute)
extract_sequence() (in module pyproteome.data_sets)
(in module pyproteome.data_sets.sequence)
F
fetch_data_set() (in module pyproteome.pride)
fetch_uniprot_data() (in module pyproteome.pypuniprot)
FIGURES_DIR (in module pyproteome.paths)
FIGURES_NAME (in module pyproteome.paths)
filter() (pyproteome.data_sets.data_set.DataSet method)
(pyproteome.data_sets.DataSet method)
filter_fn() (in module pyproteome.pathways)
filter_gene_sets() (in module pyproteome.pathways.enrichments)
filter_vals() (in module pyproteome.pathways.enrichments)
find_base_dir() (in module pyproteome.paths)
fix_channel_names() (pyproteome.data_sets.data_set.DataSet method)
(pyproteome.data_sets.DataSet method)
flatten_list() (in module pyproteome.utils)
flatten_set() (in module pyproteome.utils)
format_title() (in module pyproteome.motifs.plogo)
fuzzy_find() (in module pyproteome.utils)
G
generate_logos() (in module pyproteome.motifs.phosphosite)
generate_n_mers() (in module pyproteome.motifs)
(in module pyproteome.motifs.motif)
genes (pyproteome.data_sets.data_set.DataSet attribute)
(pyproteome.data_sets.DataSet attribute)
(pyproteome.data_sets.Proteins attribute)
(pyproteome.data_sets.protein.Proteins attribute)
get_channel_levels() (in module pyproteome.levels)
get_data() (in module pyproteome.cluster.clusterer)
(in module pyproteome.motifs.phosphosite)
(pyproteome.data_sets.DataSet method)
(pyproteome.data_sets.data_set.DataSet method)
get_gene_changes() (in module pyproteome.pathways.enrichments)
get_go_ids() (in module pyproteome.pathways.go)
get_groups() (pyproteome.data_sets.data_set.DataSet method)
(pyproteome.data_sets.DataSet method)
get_gskb_pathways() (in module pyproteome.pathways.gskb)
get_mods() (pyproteome.data_sets.modification.Modifications method)
(pyproteome.data_sets.Modifications method)
get_msigdb_pathways() (in module pyproteome.pathways.msigdb)
get_name() (in module pyproteome.utils)
get_nmer_args() (in module pyproteome.motifs.motif)
get_pathway_common() (in module pyproteome.pathways.pathwayscommon)
get_pathways() (in module pyproteome.pathways)
get_phosphomap_data() (in module pyproteome.pathways.psp)
get_phosphoreg_data() (in module pyproteome.pathways.psp)
get_phosphosite() (in module pyproteome.pathways.psp)
get_phosphosite_regulation() (in module pyproteome.pathways.psp)
get_ptmsigdb() (in module pyproteome.pathways.ptmsigdb)
get_samples() (pyproteome.data_sets.data_set.DataSet method)
(pyproteome.data_sets.DataSet method)
get_uniprot_data() (in module pyproteome.pypuniprot)
get_wikipathways() (in module pyproteome.pathways.wikipathways)
get_wikipathways_psites() (in module pyproteome.pathways.wikipathways)
gsea() (in module pyproteome.pathways)
H
hierarchical_clusters() (in module pyproteome.cluster.plot)
hierarchical_heatmap() (in module pyproteome.analysis.heatmap)
I
icelogo() (in module pyproteome.motifs.icelogo)
import_all() (in module pyproteome)
intensity_data (pyproteome.data_sets.data_set.DataSet attribute)
(pyproteome.data_sets.DataSet attribute)
inter_normalize() (pyproteome.data_sets.data_set.DataSet method)
(pyproteome.data_sets.DataSet method)
INV_ORGANISM_MAPPING (in module pyproteome.species)
is_labeled (pyproteome.data_sets.Sequence attribute)
(pyproteome.data_sets.sequence.Sequence attribute)
is_underlabeled (pyproteome.data_sets.Sequence attribute)
(pyproteome.data_sets.sequence.Sequence attribute)
K
kde_max() (in module pyproteome.levels)
L
LABEL_NAME_TARGETS (in module pyproteome.data_sets.modification)
letter (pyproteome.data_sets.Modification attribute)
(pyproteome.data_sets.modification.Modification attribute)
list_data_set() (in module pyproteome.pride)
load() (in module pyproteome.utils)
load_all_data() (in module pyproteome.data_sets)
(in module pyproteome.data_sets.data_set)
load_camv_validation() (in module pyproteome.camv)
load_psms() (in module pyproteome.loading)
log_stats() (pyproteome.data_sets.data_set.DataSet method)
(pyproteome.data_sets.DataSet method)
logo() (in module pyproteome.motifs.logo)
M
make_folder() (in module pyproteome.utils)
make_logo() (in module pyproteome.motifs.icelogo)
(in module pyproteome.motifs.logo)
(in module pyproteome.motifs.plogo)
(in module pyproteome.motifs.weblogo)
makedirs() (in module pyproteome.utils)
match() (pyproteome.motifs.motif.Motif method)
memoize() (in module pyproteome.utils)
merge_all_data() (in module pyproteome.data_sets)
(in module pyproteome.data_sets.data_set)
merge_data() (in module pyproteome.data_sets)
(in module pyproteome.data_sets.data_set)
merge_duplicates() (pyproteome.data_sets.data_set.DataSet method)
(pyproteome.data_sets.DataSet method)
merge_proteins() (in module pyproteome.data_sets)
(in module pyproteome.data_sets.data_set)
merge_subsequences() (pyproteome.data_sets.data_set.DataSet method)
(pyproteome.data_sets.DataSet method)
MERGE_UNDERLABELED (in module pyproteome.data_sets.modification)
MIN_PERIODS (in module pyproteome.pathways.enrichments)
Modification (class in pyproteome.data_sets)
(class in pyproteome.data_sets.modification)
Modifications (class in pyproteome.data_sets)
(class in pyproteome.data_sets.modification)
Motif (class in pyproteome.motifs.motif)
motif (pyproteome.motifs.motif.Motif attribute)
motif_enrichment() (in module pyproteome.motifs.motif)
motif_table() (in module pyproteome.analysis.tables)
MS_RAW_DIR (in module pyproteome.paths)
MS_RAW_NAME (in module pyproteome.paths)
MS_SEARCHED_DIR (in module pyproteome.paths)
MS_SEARCHED_NAME (in module pyproteome.paths)
N
norm() (in module pyproteome.utils)
norm_all_data() (in module pyproteome.data_sets)
(in module pyproteome.data_sets.data_set)
norm_cmp_groups() (pyproteome.data_sets.data_set.DataSet method)
(pyproteome.data_sets.DataSet method)
normalize() (pyproteome.data_sets.data_set.DataSet method)
(pyproteome.data_sets.DataSet method)
O
ORGANISM_MAPPING (in module pyproteome.species)
P
pairwise_children() (pyproteome.motifs.motif.Motif method)
pca() (in module pyproteome.cluster.plot)
pdf() (pyproteome.pathways.enrichments.PrPDF method)
phosphosites (pyproteome.data_sets.data_set.DataSet attribute)
(pyproteome.data_sets.DataSet attribute)
photon() (in module pyproteome.pathways.photon_ptm)
PICKLE_DIR (in module pyproteome.utils)
plogo() (in module pyproteome.motifs.plogo)
plot() (in module pyproteome.analysis.plot)
plot_all() (in module pyproteome.analysis.plot)
plot_all_clusters() (in module pyproteome.cluster.plot)
plot_cluster() (in module pyproteome.cluster.plot)
plot_correlations() (in module pyproteome.pathways.plot)
plot_enrichment() (in module pyproteome.pathways.plot)
plot_group() (in module pyproteome.analysis.plot)
plot_gsea() (in module pyproteome.pathways.plot)
plot_nes() (in module pyproteome.pathways.plot)
plot_nes_dist() (in module pyproteome.pathways.plot)
plot_together() (in module pyproteome.analysis.plot)
plot_volcano() (in module pyproteome.analysis.volcano)
plot_volcano_filtered() (in module pyproteome.analysis.volcano)
plot_volcano_labels() (in module pyproteome.analysis.volcano)
prefetch_all_msf_uniprot() (in module pyproteome.pypuniprot)
prefetch_all_uniprot() (in module pyproteome.pypuniprot)
Protein (class in pyproteome.data_sets)
(class in pyproteome.data_sets.protein)
ProteinMatch (class in pyproteome.data_sets)
(class in pyproteome.data_sets.sequence)
Proteins (class in pyproteome.data_sets)
(class in pyproteome.data_sets.protein)
PrPDF (class in pyproteome.pathways.enrichments)
psea() (in module pyproteome.pathways)
ptmsigdb_changes_table() (in module pyproteome.analysis.tables)
pyproteome (module)
pyproteome.analysis (module)
pyproteome.analysis.correlation (module)
pyproteome.analysis.heatmap (module)
pyproteome.analysis.plot (module)
pyproteome.analysis.protein (module)
pyproteome.analysis.tables (module)
pyproteome.analysis.volcano (module)
pyproteome.camv (module)
pyproteome.cluster (module)
pyproteome.cluster.auto (module)
pyproteome.cluster.clusterer (module)
pyproteome.cluster.plot (module)
pyproteome.data_sets (module)
pyproteome.data_sets.constand (module)
pyproteome.data_sets.data_set (module)
pyproteome.data_sets.modification (module)
pyproteome.data_sets.protein (module)
pyproteome.data_sets.sequence (module)
pyproteome.discoverer (module)
pyproteome.levels (module)
pyproteome.loading (module)
pyproteome.motifs (module)
pyproteome.motifs.icelogo (module)
pyproteome.motifs.logo (module)
pyproteome.motifs.motif (module)
pyproteome.motifs.neighborhood (module)
pyproteome.motifs.phosphosite (module)
pyproteome.motifs.plogo (module)
pyproteome.motifs.weblogo (module)
pyproteome.paths (module)
pyproteome.pathways (module)
pyproteome.pathways.enrichments (module)
pyproteome.pathways.go (module)
pyproteome.pathways.gskb (module)
pyproteome.pathways.msigdb (module)
pyproteome.pathways.pathwayscommon (module)
pyproteome.pathways.photon_ptm (module)
pyproteome.pathways.plot (module)
pyproteome.pathways.plsr (module)
pyproteome.pathways.psp (module)
pyproteome.pathways.ptmsigdb (module)
pyproteome.pathways.wikipathways (module)
pyproteome.pride (module)
pyproteome.pypuniprot (module)
pyproteome.species (module)
pyproteome.utils (module)
pyproteome.version (module)
R
read_discoverer_msf() (in module pyproteome.discoverer)
rename_channels() (pyproteome.data_sets.data_set.DataSet method)
(pyproteome.data_sets.DataSet method)
run_motif_enrichment() (in module pyproteome.motifs.motif)
S
samples (pyproteome.data_sets.data_set.DataSet attribute)
(pyproteome.data_sets.DataSet attribute)
save() (in module pyproteome.utils)
Sequence (class in pyproteome.data_sets)
(class in pyproteome.data_sets.sequence)
set_base_dir() (in module pyproteome.paths)
sf() (pyproteome.pathways.enrichments.PrPDF method)
shape (pyproteome.data_sets.data_set.DataSet attribute)
(pyproteome.data_sets.DataSet attribute)
show_cluster() (in module pyproteome.cluster.plot)
show_peptide_clusters() (in module pyproteome.cluster.plot)
simulate_es_s_pi() (in module pyproteome.pathways.enrichments)
skip_labels() (pyproteome.data_sets.modification.Modifications method)
(pyproteome.data_sets.Modifications method)
ssgsea() (in module pyproteome.pathways)
sspsea() (in module pyproteome.pathways)
stars() (in module pyproteome.utils)
T
to_tuple() (pyproteome.data_sets.Modification method)
(pyproteome.data_sets.ProteinMatch method)
(pyproteome.data_sets.Sequence method)
(pyproteome.data_sets.modification.Modification method)
(pyproteome.data_sets.sequence.ProteinMatch method)
(pyproteome.data_sets.sequence.Sequence method)
U
update_correlation() (in module pyproteome.data_sets)
(in module pyproteome.data_sets.data_set)
update_group_changes() (pyproteome.data_sets.data_set.DataSet method)
(pyproteome.data_sets.DataSet method)
update_pairwise_corr() (in module pyproteome.data_sets.data_set)
V
version (in module pyproteome.version)
vip() (in module pyproteome.pathways.plsr)
W
which() (in module pyproteome.utils)
write_csv() (in module pyproteome.analysis.tables)
write_full_tables() (in module pyproteome.analysis.tables)
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pyproteome version documentation
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