ProteoGyver
Contents:
Proteogyver
Example Proteomics usecase for ProteoGyver
Example Interactomcis usecase for ProteoGyver
ProteoGyver User Guide
Code Reference
ProteoGyver
Index
Index
A
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B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
Z
A
add_bait_column() (in module app.components.interactomics)
add_column() (in module app.components.db_functions)
add_crapome() (in module app.components.interactomics)
add_multiple_records() (in module app.components.db_functions)
add_record() (in module app.components.db_functions)
additional_controls (app.pipeline_module.pipeline_batch.BatchConfig attribute)
analyze() (in module utils.MSParser.MSparser)
anova() (in module app.components.quick_stats)
app
module
app (in module app.app)
app.app
module
app.components
module
app.components.api_tools
module
app.components.api_tools.apitools
module
app.components.api_tools.biogrid
module
app.components.api_tools.intact
module
app.components.api_tools.uniprot
module
app.components.cleanup_tasks
module
app.components.db_functions
module
app.components.enrichment
module
app.components.enrichment.pantherdb
module
app.components.EnrichmentAdmin
module
app.components.figure_functions
module
app.components.figures
module
app.components.figures.bar_graph
module
app.components.figures.before_after_plot
module
app.components.figures.color_tools
module
app.components.figures.commonality_graph
module
app.components.figures.comparative_plot
module
app.components.figures.cvplot
module
app.components.figures.figure_legends
module
app.components.figures.heatmaps
module
app.components.figures.histogram
module
app.components.figures.imputation_histogram
module
app.components.figures.network_plot
module
app.components.figures.reproducibility_graph
module
app.components.figures.scatter
module
app.components.figures.tic_graph
module
app.components.figures.volcano_plot
module
app.components.file_upload_api
module
app.components.interactomics
module
app.components.mathparser
module
app.components.matrix_functions
module
app.components.ms_microscopy
module
app.components.MS_run_json_parser
module
app.components.parsing
module
app.components.proteomics
module
app.components.qc_analysis
module
app.components.quick_stats
module
app.components.text_handling
module
app.components.tools
module
app.components.tools.R_tools
module
app.components.tools.utils
module
app.components.tooltips
module
app.components.ui_components
module
app.database_admin
module
app.database_updater
module
app.element_styles
module
app.embedded_page_updater
module
app.pages
module
app.pipeline_module
module
app.pipeline_module.batch_data_store_builder
module
app.pipeline_module.batch_figure_builder_from_divs
module
app.pipeline_module.pipeline_batch
module
app.pipeline_module.pipeline_from_toml
module
app.pipeline_module.pipeline_input_watcher
module
app.resources
module
app.resources.get_cpu_count
module
app.run_as_pipeline
module
B
bar_plot() (in module app.components.figures.bar_graph)
BatchConfig (class in app.pipeline_module.pipeline_batch)
bits (app.components.figures.commonality_graph.Intersection attribute)
build_analysis_divs_from_saved_divs() (in module app.pipeline_module.batch_figure_builder_from_divs)
build_data_stores_from_batch_output() (in module app.pipeline_module.batch_data_store_builder)
build_interactomics_data_stores() (in module app.pipeline_module.batch_data_store_builder)
build_proteomics_data_stores() (in module app.pipeline_module.batch_data_store_builder)
build_qc_data_stores() (in module app.pipeline_module.batch_data_store_builder)
build_replicate_colors_stores() (in module app.pipeline_module.batch_data_store_builder)
build_upload_data_store() (in module app.pipeline_module.batch_data_store_builder)
C
calculate_auc() (in module utils.MSParser.MSparser)
celery_app (in module app.app)
check_bait() (in module app.components.parsing)
check_comparison_file() (in module app.components.parsing)
check_numeric() (in module app.components.parsing)
check_required_columns() (in module app.components.parsing)
check_sample_table_column() (in module app.components.parsing)
checklist() (in module app.components.ui_components)
chosen_enrichments (app.pipeline_module.pipeline_batch.BatchConfig attribute)
clean_column_name() (in module app.components.parsing)
clean_database() (in module app.database_admin)
clean_sample_names() (in module app.components.parsing)
clean_text() (in module app.components.text_handling)
clustermap() (in module app.components.proteomics)
common_proteins() (in module app.components.qc_analysis)
commonality_plot() (in module app.components.qc_analysis)
comparison_file (app.pipeline_module.pipeline_batch.BatchConfig attribute)
compute_zscore() (in module app.components.matrix_functions)
compute_zscore_based_deviation_from_control() (in module app.components.matrix_functions)
control_group (app.pipeline_module.pipeline_batch.BatchConfig attribute)
count_intercepts() (in module utils.MSParser.MSparser)
count_knowns() (in module app.components.interactomics)
count_per_sample() (in module app.components.matrix_functions)
count_plot() (in module app.components.qc_analysis)
coverage_plot() (in module app.components.qc_analysis)
crapome_fc_threshold (app.pipeline_module.pipeline_batch.BatchConfig attribute)
crapome_percentage_threshold (app.pipeline_module.pipeline_batch.BatchConfig attribute)
crapome_sets (app.pipeline_module.pipeline_batch.BatchConfig attribute)
create_connection() (in module app.components.db_functions)
create_data_store_component() (in module app.pipeline_module.batch_data_store_builder)
create_dummy_list_txt() (in module app.components.interactomics)
create_navbar() (in module app.app)
create_page_file() (in module app.embedded_page_updater)
create_sqlite_from_schema() (in module app.database_admin)
create_upset_figure() (in module app.components.figures.commonality_graph)
D
darken() (in module app.components.figures.color_tools)
dash_to_wire() (in module app.pipeline_module.pipeline_batch)
data_store_export_configuration (in module app.components.infra)
DATA_STORE_IDS (in module app.components.infra)
data_table_path (app.pipeline_module.pipeline_batch.BatchConfig attribute)
deduplicate_nested_dicts() (in module utils.MSParser.parse_thermo)
deduplicate_str_dataframe_by_index() (in module app.components.api_tools.biogrid)
deep_merge() (in module app.components.tools.utils)
delete_multiple_records() (in module app.components.db_functions)
delete_record() (in module app.components.db_functions)
delete_samples() (in module app.components.parsing)
differential() (in module app.components.quick_stats)
differential_abundance() (in module app.components.proteomics)
dig_dict() (in module app.components.tools.utils)
discard_samples_checklist() (in module app.components.ui_components)
distribution_plot() (in module app.components.qc_analysis)
do_ms_microscopy() (in module app.components.interactomics)
do_network() (in module app.components.interactomics)
do_pca() (in module app.components.matrix_functions)
do_update() (in module app.components.api_tools.biogrid)
(in module app.components.api_tools.intact)
download_full_uniprot_for_organism() (in module app.components.api_tools.uniprot)
download_intact_ftp() (in module app.components.api_tools.intact)
download_uniprot_chunks() (in module app.components.api_tools.uniprot)
download_uniprot_for_database() (in module app.components.api_tools.uniprot)
download_uniprot_pagination_url() (in module app.components.api_tools.uniprot)
draw_clustergram() (in module app.components.figures.heatmaps)
draw_localization_heatmap() (in module app.components.ms_microscopy)
draw_localization_plot() (in module app.components.ms_microscopy)
drop_table() (in module app.components.db_functions)
dump_full_database_to_csv() (in module app.components.db_functions)
E
enrich() (app.components.enrichment.pantherdb.handler method)
(in module app.components.interactomics)
enrich_all() (app.components.EnrichmentAdmin.EnrichmentAdmin method)
enrichment_legend() (in module app.components.figures.figure_legends)
EnrichmentAdmin (class in app.components.EnrichmentAdmin)
eval_() (app.components.mathparser.MathParser method)
expand_path() (in module app.components.tools.utils)
expand_paths() (in module app.components.tools.utils)
export_snapshot() (in module app.components.db_functions)
F
fc_threshold (app.pipeline_module.pipeline_batch.BatchConfig attribute)
figure_export_directories (in module app.components.infra)
figure_template (app.pipeline_module.pipeline_batch.BatchConfig attribute)
filter_chunk() (in module app.components.api_tools.biogrid)
(in module app.components.api_tools.intact)
filter_controls_by_similarity() (in module app.components.interactomics)
filter_missing() (in module app.components.matrix_functions)
force_supervenn (app.pipeline_module.pipeline_batch.BatchConfig attribute)
format_data() (in module app.components.parsing)
format_sample_group_name() (in module app.components.parsing)
G
generate_commonality_container() (in module app.components.qc_analysis)
generate_database_table_templates_as_tsvs() (in module app.components.db_functions)
generate_graphs() (in module app.components.figures.volcano_plot)
generate_msmic_dataframes() (in module app.components.ms_microscopy)
generate_pandas() (in module app.components.api_tools.biogrid)
(in module app.components.api_tools.intact)
generate_replicate_name() (in module app.components.parsing)
generate_saint_container() (in module app.components.interactomics)
generic_tooltip() (in module app.components.tooltips)
get_all_props() (in module app.components.infra)
get_all_types() (in module app.components.infra)
get_assigned_colors() (in module app.components.figures.color_tools)
get_available() (app.components.enrichment.pantherdb.handler method)
(app.components.EnrichmentAdmin.EnrichmentAdmin method)
(in module app.components.api_tools.biogrid)
(in module app.components.api_tools.intact)
get_common_data() (in module app.components.quick_stats)
get_commonality_pdf_data() (in module app.pipeline_module.batch_figure_builder_from_divs)
get_comparative_data() (in module app.components.quick_stats)
get_contaminants() (in module app.components.db_functions)
get_count_data() (in module app.components.quick_stats)
get_coverage_data() (in module app.components.quick_stats)
get_cut_colors() (in module app.components.figures.color_tools)
get_cytoscape_container() (in module app.components.figures.network_plot)
get_cytoscape_elements_and_ints() (in module app.components.figures.network_plot)
get_database_versions() (in module app.components.db_functions)
get_dataframe_differences() (in module app.database_updater)
get_default() (app.components.EnrichmentAdmin.EnrichmentAdmin method)
get_default_panel() (app.components.enrichment.pantherdb.handler method)
get_default_uniprot_column_map() (in module app.components.api_tools.uniprot)
get_directory_size() (in module utils.MSParser.parse_timstof)
get_disabled() (app.components.EnrichmentAdmin.EnrichmentAdmin method)
get_distribution_title() (in module app.components.parsing)
get_external_versions() (in module app.database_admin)
get_files_newer_than() (in module app.components.api_tools.apitools)
get_final_df() (in module app.components.api_tools.biogrid)
(in module app.components.api_tools.intact)
get_from_table() (in module app.components.db_functions)
get_from_table_by_list_criteria() (in module app.components.db_functions)
get_from_table_match_with_priority() (in module app.components.db_functions)
get_full_table_as_pd() (in module app.components.db_functions)
get_ids() (in module app.components.api_tools.intact)
get_iso() (in module app.components.api_tools.intact)
get_last_update() (in module app.components.db_functions)
get_latest() (in module app.components.api_tools.biogrid)
(in module app.components.api_tools.intact)
get_max() (in module app.components.figures.reproducibility_graph)
get_mean_data() (in module app.components.quick_stats)
get_method_annotation() (in module app.components.api_tools.biogrid)
get_na_data() (in module app.components.quick_stats)
get_nbibfile() (in module app.components.api_tools.apitools)
get_newest_file() (in module app.components.api_tools.apitools)
get_org() (in module app.components.api_tools.intact)
get_pantherdb_datasets() (app.components.enrichment.pantherdb.handler method)
get_pub_ref() (in module app.components.api_tools.apitools)
get_reproducibility_dataframe() (in module app.components.figures.reproducibility_graph)
get_saint_matrix() (in module app.components.interactomics)
get_save_location() (in module app.components.api_tools.apitools)
get_scantypes() (in module utils.MSParser.parse_thermo)
get_stylesheet() (in module app.components.figures.network_plot)
get_sum_data() (in module app.components.quick_stats)
get_table_column_names() (in module app.components.db_functions)
get_timestamp() (in module app.components.api_tools.apitools)
get_traces() (in module utils.MSParser.parse_thermo)
(in module utils.MSParser.parse_timstof)
get_uniprot_column_map() (in module app.components.api_tools.uniprot)
get_upid() (in module app.components.api_tools.biogrid)
guess_controls() (in module app.components.parsing)
H
handle_and_split_save() (in module app.components.api_tools.biogrid)
(in module app.components.api_tools.intact)
handle_data() (in module utils.MSParser.MSparser)
handle_merg_chunk() (in module app.database_updater)
handle_mods() (in module app.database_updater)
handle_mztab() (in module app.components.parsing)
handle_new() (in module app.database_updater)
handler (class in app.components.enrichment.pantherdb)
HEADER_DICT (in module app.components.ui_components)
hierarchical_clustering() (in module app.components.matrix_functions)
I
identify() (in module utils.MSParser.ms_name_identifier)
identify_columns() (in module app.components.parsing)
import_handlers() (app.components.EnrichmentAdmin.EnrichmentAdmin method)
improve_text_position() (in module app.components.figure_functions)
imputation (app.pipeline_module.pipeline_batch.BatchConfig attribute)
imputation() (in module app.components.proteomics)
impute() (in module app.components.matrix_functions)
impute_gaussian() (in module app.components.matrix_functions)
impute_minprob() (in module app.components.matrix_functions)
impute_minprob_df() (in module app.components.matrix_functions)
impute_minval() (in module app.components.matrix_functions)
impute_qrilc() (in module app.components.tools.R_tools)
impute_random_forest() (in module app.components.tools.R_tools)
interactomics_area() (in module app.components.ui_components)
interactomics_control_col() (in module app.components.ui_components)
interactomics_crapome_col() (in module app.components.ui_components)
interactomics_enrichment_col() (in module app.components.ui_components)
interactomics_inbuilt_control_col() (in module app.components.ui_components)
interactomics_input_card() (in module app.components.ui_components)
interactomics_select_top_controls_tooltip() (in module app.components.tooltips)
Intersection (class in app.components.figures.commonality_graph)
is_newer() (in module app.components.api_tools.apitools)
is_newer_available() (in module app.components.api_tools.uniprot)
is_test_db() (in module app.components.db_functions)
K
keep_batch_output (app.pipeline_module.pipeline_batch.BatchConfig attribute)
known_plot() (in module app.components.interactomics)
L
label (app.components.figures.commonality_graph.Intersection attribute)
last_update() (in module app.database_admin)
leg_rep() (in module app.components.figures.figure_legends)
list_tables() (in module app.components.db_functions)
load_config() (in module app.pipeline_module.pipeline_from_toml)
load_div_pickle() (in module app.pipeline_module.batch_figure_builder_from_divs)
load_pipeline_parameters() (in module app.pipeline_module.pipeline_from_toml)
load_toml() (in module app.components.tools.utils)
localization_graph() (in module app.components.ms_microscopy)
logger (in module app.app)
(in module app.components.interactomics)
M
main() (in module app.app)
(in module app.database_admin)
(in module app.pipeline_module.batch_figure_builder_from_divs)
(in module app.run_as_pipeline)
(in module utils.MSParser.MSparser)
main_content_div() (in module app.components.ui_components)
main_sidebar() (in module app.components.ui_components)
make_du_uploader() (in module app.components.ui_components)
make_figure() (in module app.components.figures.histogram)
(in module app.components.figures.scatter)
make_graph() (in module app.components.figures.bar_graph)
(in module app.components.figures.before_after_plot)
(in module app.components.figures.commonality_graph)
(in module app.components.figures.comparative_plot)
(in module app.components.figures.cvplot)
(in module app.components.figures.imputation_histogram)
(in module app.components.figures.reproducibility_graph)
(in module app.components.figures.scatter)
make_heatmap_graph() (in module app.components.figures.heatmaps)
make_saint_dict() (in module app.components.interactomics)
map_intensity() (in module app.components.interactomics)
map_protein_info() (in module app.components.db_functions)
MathParser (class in app.components.mathparser)
mean_plot() (in module app.components.qc_analysis)
median_normalize() (in module app.components.matrix_functions)
merge_multiple_string_dataframes() (in module app.database_updater)
methods_text() (in module app.components.api_tools.biogrid)
(in module app.components.api_tools.intact)
(in module app.components.api_tools.uniprot)
missing_plot() (in module app.components.qc_analysis)
missing_values_in_other_samples() (in module app.components.proteomics)
modals() (in module app.components.ui_components)
modify_multiple_records() (in module app.components.db_functions)
modify_record() (in module app.components.db_functions)
module
app
app.app
app.components
app.components.api_tools
app.components.api_tools.apitools
app.components.api_tools.biogrid
app.components.api_tools.intact
app.components.api_tools.uniprot
app.components.cleanup_tasks
app.components.db_functions
app.components.enrichment
app.components.enrichment.pantherdb
app.components.EnrichmentAdmin
app.components.figure_functions
app.components.figures
app.components.figures.bar_graph
app.components.figures.before_after_plot
app.components.figures.color_tools
app.components.figures.commonality_graph
app.components.figures.comparative_plot
app.components.figures.cvplot
app.components.figures.figure_legends
app.components.figures.heatmaps
app.components.figures.histogram
app.components.figures.imputation_histogram
app.components.figures.network_plot
app.components.figures.reproducibility_graph
app.components.figures.scatter
app.components.figures.tic_graph
app.components.figures.volcano_plot
app.components.file_upload_api
app.components.interactomics
app.components.mathparser
app.components.matrix_functions
app.components.ms_microscopy
app.components.MS_run_json_parser
app.components.parsing
app.components.proteomics
app.components.qc_analysis
app.components.quick_stats
app.components.text_handling
app.components.tools
app.components.tools.R_tools
app.components.tools.utils
app.components.tooltips
app.components.ui_components
app.database_admin
app.database_updater
app.element_styles
app.embedded_page_updater
app.pages
app.pipeline_module
app.pipeline_module.batch_data_store_builder
app.pipeline_module.batch_figure_builder_from_divs
app.pipeline_module.pipeline_batch
app.pipeline_module.pipeline_from_toml
app.pipeline_module.pipeline_input_watcher
app.resources
app.resources.get_cpu_count
app.run_as_pipeline
utils.MSParser
utils.MSParser.ms_name_identifier
utils.MSParser.MSparser
utils.MSParser.parse_thermo
utils.MSParser.parse_timstof
N
n_controls (app.pipeline_module.pipeline_batch.BatchConfig attribute)
na_filter() (in module app.components.proteomics)
na_filter_percent (app.pipeline_module.pipeline_batch.BatchConfig attribute)
na_filter_type (app.pipeline_module.pipeline_batch.BatchConfig attribute)
na_tooltip() (in module app.components.tooltips)
navbar() (in module app.components.ui_components)
nearest_tooltip() (in module app.components.tooltips)
network_display_data() (in module app.components.interactomics)
nice_name (app.components.enrichment.pantherdb.handler property)
normalization (app.pipeline_module.pipeline_batch.BatchConfig attribute)
normalization() (in module app.components.proteomics)
normalize() (in module app.components.matrix_functions)
normalize_key() (in module app.components.tools.utils)
O
only_latest_date() (in module app.components.api_tools.intact)
outdir (app.pipeline_module.pipeline_batch.BatchConfig attribute)
P
p_threshold (app.pipeline_module.pipeline_batch.BatchConfig attribute)
panel_to_usable() (app.components.enrichment.pantherdb.handler method)
parse() (app.components.mathparser.MathParser method)
parse_comparisons() (in module app.components.parsing)
parse_d() (in module utils.MSParser.MSparser)
parse_data_file() (in module app.components.parsing)
parse_embed_file() (in module app.embedded_page_updater)
parse_file() (in module utils.MSParser.parse_thermo)
(in module utils.MSParser.parse_timstof)
parse_parameters() (in module app.components.parsing)
parse_raw() (in module utils.MSParser.MSparser)
parse_sample_table() (in module app.components.parsing)
parse_tic_data() (in module app.components.qc_analysis)
parse_timestamp_from_str() (in module app.components.api_tools.apitools)
pca() (in module app.components.interactomics)
(in module app.components.proteomics)
perc_cvplot() (in module app.components.proteomics)
plot_formats (app.pipeline_module.pipeline_batch.BatchConfig attribute)
post_saint_container() (in module app.components.ui_components)
prefix_relative_paths() (in module app.components.tools.utils)
prepare_controls() (in module app.components.interactomics)
prepare_crapome() (in module app.components.interactomics)
proteomics_area() (in module app.components.ui_components)
proteomics_input_card() (in module app.components.ui_components)
proximity_filtering (app.pipeline_module.pipeline_batch.BatchConfig attribute)
Q
qc_area() (in module app.components.ui_components)
quantile_normalize() (in module app.components.matrix_functions)
R
range_input() (in module app.components.ui_components)
ranked_dist() (in module app.components.matrix_functions)
ranked_dist_n_per_run() (in module app.components.matrix_functions)
read_data_from_content() (in module app.components.parsing)
read_df_from_content() (in module app.components.parsing)
read_dia_nn() (in module app.components.parsing)
read_file_chunks() (in module app.components.api_tools.biogrid)
(in module app.components.api_tools.intact)
read_folder_chunks() (in module app.components.api_tools.biogrid)
(in module app.components.api_tools.intact)
read_fragpipe() (in module app.components.parsing)
read_matrix() (in module app.components.parsing)
read_toml() (in module app.components.tools.utils)
(in module utils.MSParser.MSparser)
register_file_upload_api() (in module app.components.file_upload_api)
remove_accent_characters() (in module app.components.text_handling)
(in module utils.MSParser.MSparser)
remove_all_na() (in module app.components.parsing)
remove_column() (in module app.components.db_functions)
remove_common_contaminants (app.pipeline_module.pipeline_batch.BatchConfig attribute)
remove_duplicate_protein_groups() (in module app.components.parsing)
remove_file_path() (in module app.components.parsing)
remove_filepath_from_columns() (in module app.components.parsing)
remove_from_table() (in module app.components.parsing)
remove_rawfile_ending() (in module app.components.parsing)
(in module utils.MSParser.MSparser)
remove_unwanted_colors() (in module app.components.figures.color_tools)
rename_column() (in module app.components.db_functions)
rename_columns_and_update_expdesign() (in module app.components.parsing)
rename_replicates (app.pipeline_module.pipeline_batch.BatchConfig attribute)
replace_accent_and_special_characters() (in module app.components.text_handling)
replace_special_characters() (in module app.components.text_handling)
(in module utils.MSParser.MSparser)
reproducibility_plot() (in module app.components.qc_analysis)
rescue_enabled (app.pipeline_module.pipeline_batch.BatchConfig attribute)
rescue_tooltip() (in module app.components.tooltips)
retrieve_pantherdb_gene_classification() (app.components.enrichment.pantherdb.handler method)
retrieve_protein_group() (in module app.components.api_tools.uniprot)
retrieve_uniprot() (in module app.components.api_tools.uniprot)
reverse_log2() (in module app.components.matrix_functions)
rgba_to_hex() (in module app.components.figures.color_tools)
roundup() (in module utils.MSParser.parse_thermo)
run_batch_pipeline() (in module app.run_as_pipeline)
run_panther_overrepresentation_analysis() (app.components.enrichment.pantherdb.handler method)
run_pipeline() (in module app.pipeline_module.pipeline_batch)
run_rscript() (in module app.components.tools.R_tools)
run_saint() (in module app.components.interactomics)
S
saint_bfdr_threshold (app.pipeline_module.pipeline_batch.BatchConfig attribute)
saint_cmd() (in module app.components.interactomics)
saint_counts() (in module app.components.interactomics)
saint_filtering() (in module app.components.interactomics)
saint_filtering_container() (in module app.components.ui_components)
saint_histogram() (in module app.components.interactomics)
saint_legend() (in module app.components.figures.figure_legends)
sample_table_path (app.pipeline_module.pipeline_batch.BatchConfig attribute)
sanitize_for_database_use() (in module app.components.text_handling)
save_batch_data_using_infra() (in module app.pipeline_module.batch_data_store_builder)
save_batch_figures_using_saved_divs() (in module app.pipeline_module.batch_figure_builder_from_divs)
save_data_stores() (in module app.components.infra)
save_figures() (in module app.components.infra)
save_input_information() (in module app.components.infra)
save_toml() (in module app.components.tools.utils)
sdrf_to_table() (in module app.components.parsing)
server (in module app.app)
size (app.components.figures.commonality_graph.Intersection attribute)
split_and_save_by_prefix() (in module app.components.api_tools.biogrid)
(in module app.components.api_tools.intact)
stream_flattened_rows() (in module app.database_updater)
sum_plot() (in module app.components.qc_analysis)
T
table_of_contents() (in module app.components.ui_components)
test_type (app.pipeline_module.pipeline_batch.BatchConfig attribute)
test_type_tooltip() (in module app.components.tooltips)
tic_figure() (in module app.components.figures.tic_graph)
toggle_navbar_collapse() (in module app.app)
tweak_fig_size_hw() (in module app.components.ms_microscopy)
U
unique_only (app.pipeline_module.pipeline_batch.BatchConfig attribute)
unmix_dtypes() (in module app.components.parsing)
update() (in module app.components.api_tools.biogrid)
(in module app.components.api_tools.intact)
(in module app.components.api_tools.uniprot)
update_database() (in module app.database_updater)
update_external_data() (in module app.database_updater)
update_knowns() (in module app.database_updater)
update_log_table() (in module app.database_updater)
update_nested_dict() (in module app.components.parsing)
update_pages() (in module app.embedded_page_updater)
update_table_with_file() (in module app.database_updater)
update_uniprot() (in module app.database_updater)
update_version_table() (in module app.database_updater)
upload_area() (in module app.components.ui_components)
upload_data_stores() (in module app.components.infra)
uploaded_controls (app.pipeline_module.pipeline_batch.BatchConfig attribute)
utils.MSParser
module
utils.MSParser.ms_name_identifier
module
utils.MSParser.MSparser
module
utils.MSParser.parse_thermo
module
utils.MSParser.parse_timstof
module
V
validate_basic_inputs() (in module app.components.parsing)
volcano_heatmap_legend() (in module app.components.figures.figure_legends)
volcano_plot() (in module app.components.figures.volcano_plot)
volcano_plot_legend() (in module app.components.figures.figure_legends)
vsn() (in module app.components.tools.R_tools)
W
workflow (app.pipeline_module.pipeline_batch.BatchConfig attribute)
workflow_area() (in module app.components.ui_components)
working_data_stores() (in module app.components.infra)
Z
zipdir() (in module app.components.tools.utils)