prolfqua-package	prolfqua-package
.get_robscales	dot-get_robscales
.lfqdata_to_elist	dot-lfqdata_to_elist
.make_progress	dot-make_progress
.resolve_weights	dot-resolve_weights
adjust_p_values	adjust_p_values
AggregateLimpa	AggregateLimpa
AggregateMedpolish	AggregateMedpolish
AggregateRlm	AggregateRlm
AggregateTopN	AggregateTopN
aggregate_intensity_top_n	aggregate_intensity_top_n
AggregatorBase	AggregatorBase
AnalysisConfiguration	AnalysisConfiguration
annotation_add_contrasts	annotation_add_contrasts
AnovaExtractor	AnovaExtractor
apply_to_response_matrix	apply_to_response_matrix
build_contrast_analysis	build_contrast_analysis
build_model	build_model
build_model_glm_peptide	build_model_glm_peptide
build_model_glm_protein	build_model_glm_protein
build_model_impute	build_model_impute
build_model_limma	build_model_limma
build_model_limma_impute	build_model_limma_impute
build_model_limma_voom	build_model_limma_voom
build_model_limma_voom_impute	build_model_limma_voom_impute
build_model_limpa	build_model_limpa
build_model_logistf	build_model_logistf
center_to_reference_cfg	center_to_reference_cfg
complete_cases	complete_cases
compute_borrowed_variance	compute_borrowed_variance
compute_borrowed_variance_limma	compute_borrowed_variance_limma
compute_contrast	compute_contrast
compute_lmer_contrast	compute_lmer_contrast
compute_pooled	pooled_var
ContrastConfiguration	ContrastConfiguration
Contrasts	Contrasts
ContrastsBinomialNestedFacade	ContrastsBinomialNestedFacade
ContrastsDEqMSFacade	ContrastsDEqMSFacade
ContrastsDEqMSVoomFacade	ContrastsDEqMSVoomFacade
ContrastsFacadeBase	ContrastsFacadeBase
ContrastsFirth	ContrastsFirth
ContrastsFirthFacade	ContrastsFirthFacade
ContrastsFirthNestedFacade	ContrastsFirthNestedFacade
ContrastsInterface	ContrastsInterface
ContrastsLimma	ContrastsLimma
ContrastsLimmaFacade	ContrastsLimmaFacade
ContrastsLimmaImputeFacade	ContrastsLimmaImputeFacade
ContrastsLimmaVoomFacade	ContrastsLimmaVoomFacade
ContrastsLimmaVoomImputeFacade	ContrastsLimmaVoomImputeFacade
ContrastsLimpaFacade	ContrastsLimpaFacade
ContrastsLimpaNestedFacade	ContrastsLimpaNestedFacade
ContrastsLmerNestedFacade	ContrastsLmerNestedFacade
ContrastsLMFacade	ContrastsLMFacade
ContrastsLMImputeFacade	ContrastsLMImputeFacade
ContrastsModerated	ContrastsModerated
ContrastsModeratedDEqMS	ContrastsModeratedDEqMS
ContrastsPlotter	ContrastsPlotter
ContrastsRfitFacade	ContrastsRfitFacade
ContrastsRfitImputeFacade	ContrastsRfitImputeFacade
ContrastsRLMFacade	ContrastsRLMFacade
ContrastsROPECA	ContrastsROPECA
ContrastsROPECANestedFacade	ContrastsROPECANestedFacade
ContrastsTable	ContrastsTable
contrasts_linfct	contrasts_linfct
data_checksummarizationrobust87	data_checksummarizationrobust87
data_checksummarizerobust69	data_checksummarizerobust69
data_ionstar	data_ionstar
df.residual.rfit_prolfqua	df.residual.rfit_prolfqua
df.residual.rlm	df.residual.rlm
encode_bin_resp	encode_bin_resp
estimate_intensity	estimate_intensity
FACADE_REGISTRY	FACADE_REGISTRY
filter_proteins_by_peptide_count	filter_proteins_by_peptide_count
find_d0_deqms	find_d0_deqms
find_package_file	find_package_file
generate_contrasts	generate_contrasts
generate_contrasts_for_factor	generate_contrasts_for_factor
get_anova_df	get_anova_df
get_complete_model_fit	get_complete_model_fit
get_contrast	get_contrast
get_p_values_pbeta	get_p_values_pbeta
get_robscales	get_robscales
get_uniprot_id_from_fasta_header	get_uniprot_id_from_fasta_header
group_label	group_label
HierarchyCountsSample	HierarchyCountsSample
hierarchy_counts	hierarchy_counts
impute_from_model	impute_from_model
impute_refit_singular	impute_refit_singular
interaction_contrasts	interaction_contrasts
INTERNAL_FUNCTIONS_BY_FAMILY	INTERNAL_FUNCTIONS_BY_FAMILY
is_contaminant	is_contaminant
is_decoy	is_decoy
level_specific_contrasts	level_specific_contrasts
LFQData	LFQData
LFQDataPlotter	LFQDataPlotter
LFQDataStats	LFQDataStats
LFQDataSummariser	LFQDataSummariser
LFQDataToSummarizedExperiment	LFQDataToSummarizedExperiment
LFQDataTransformer	LFQDataTransformer
lfq_power_t_test_proteins	lfq_power_t_test_proteins
lfq_power_t_test_quantiles_V2	lfq_power_t_test_quantiles_V2
linfct_from_model	linfct_from_model
linfct_matrix_contrasts	linfct_matrix_contrasts
list_facades	list_facades
list_to_AnalysisConfiguration	list_to_AnalysisConfiguration
list_to_ContrastConfiguration	list_to_ContrastConfiguration
lookup_facade	lookup_facade
LR_test	LR_test
main_effect_contrasts	main_effect_contrasts
make_interaction_column	make_interaction_column
make_reduced_hierarchy_config	make_reduced_hierarchy_config
matrix_to_tibble	matrix_to_tibble
merge_contrasts_results	merge_contrasts_results
missigness_histogram	missigness_histogram
MissingHelpers	MissingHelpers
missingness_per_condition	missingness_per_condition
missingness_per_condition_cumsum	missingness_per_condition_cumsum
Model	Model
ModelFirth	ModelFirth
ModelInterface	ModelInterface
ModelLimma	ModelLimma
model_analyse	model_analyse
model_summary	model_summary
moderated_p_deqms	moderated_p_deqms
moderated_p_deqms_long	moderated_p_deqms_long
moderated_p_limma	moderated_p_limma
multigroup_volcano	multigroup_volcano
new_imputed_model	new_imputed_model
nr_B_in_A	nr_B_in_A
nr_children_experiment	nr_children_experiment
nr_features_experiment	nr_features_experiment
nr_obs_sample	nr_obs_sample
PACKAGE_DATA	PACKAGE_DATA
pairs_smooth	pairs_smooth
panel_cor	panel_cor
pivot_model_contrasts_to_wide	pivot_model_contrasts_to_wide
plot_estimate	plot_estimate
plot_heatmap	plot_heatmap
plot_heatmap_cor	plot_heatmap_cor
plot_hierarchies_boxplot	plot_hierarchies_boxplot
plot_hierarchies_boxplot_df	plot_hierarchies_boxplot_df
plot_hierarchies_line	plot_hierarchies_line
plot_intensity_distribution_density	plot_intensity_distribution_violin
plot_intensity_distribution_violin	plot_intensity_distribution_violin
plot_lrt_diagnostics	plot_lrt_diagnostics
plot_na_heatmap	plot_NA_heatmap
plot_pca	plot_pca
plot_raster	plot_raster
plot_sample_correlation	plot_sample_correlation
plot_stat_density	plot_stat_density
plot_stat_density_median	plot_stat_density_median
plot_stat_violin	plot_stat_violin
plot_stat_violin_median	plot_stat_violin_median
plot_stdv_vs_mean	plot_stdv_vs_mean
poolvar	pooled_var
prolfqua	prolfqua-package
prolfqua_data	prolfqua_data
R6_extract_values	R6_extract_values
rank_peptide_by_intensity	rank_peptide_by_intensity
register_facade	register_facade
response_matrix_as_tibble	response_matrix_as_tibble
robust_scale	robust_scale
sample_subset	sample_subset
scale_with_subset	scale_with_subset
script_copy_helper_vec	script_copy_helper_vec
separate_hierarchy	separate_hierarchy
setup_analysis	setup_analysis
sigma.rfit_prolfqua	sigma.rfit_prolfqua
sigma.rlm	sigma.rlm
sim_build_models_lm	sim_build_models_lm
sim_build_models_lmer	sim_build_models_lmer
sim_build_models_logistf	sim_build_models_logistf
sim_lfq_data	sim_lfq_data
sim_lfq_data_2factor_config	sim_lfq_data_2Factor_config
sim_lfq_data_peptide_config	sim_lfq_data_peptide_config
sim_lfq_data_protein_config	sim_lfq_data_protein_config
sim_make_model_lm	sim_make_model_lm
sim_make_model_lmer	sim_make_model_lmer
StrategyBase	StrategyBase
StrategyBinomial	StrategyBinomial
StrategyLimma	StrategyLimma
StrategyLimpa	StrategyLimpa
StrategyLM	StrategyLM
StrategyLmer	StrategyLmer
StrategyLogistf	StrategyLogistf
StrategyRfit	StrategyRfit
StrategyRLM	StrategyRLM
strategy_binomial	strategy_binomial
strategy_limma	strategy_limma
strategy_limpa	strategy_limpa
strategy_lm	strategy
strategy_lmer	strategy
strategy_logistf	strategy
strategy_rfit	strategy
strategy_rlm	strategy
summarize_hierarchy	summarize_hierarchy
summarize_stats	summarize_stats
summarize_stats_factors	summarize_stats_factors
summarize_stats_quantiles	summarize_stats
summary_ROPECA_median_p_scaled	summary_ROPECA_median_p_scaled
table_facade	table_facade
table_factors	table_factors
table_factors_size	table_factors_size
tidy_to_wide_config	tidy_to_wide_config
transform_work_intensity	transform_work_intensity
upset_interaction_missing_stats	UpSet_interaction_missing_stats
upset_missing_stats	UpSet_missing_stats
vcov.rfit_prolfqua	vcov.rfit_prolfqua
volcano_plotly	volcano_Plotly
which_missing	which_missing
x5463yzwer453bbb	x5463yzwer453bbb
