.read_maxquant	read_proteingroups
.read_metabolon	read_metabolon
.read_rectangles	read_rectangles
.read_rnaseq_bams	read_rnaseq_counts
.read_rnaseq_counts	read_rnaseq_counts
.read_somascan	read_somascan
add_smiles	add_smiles
analysis	analysis
analysis,SummarizedExperiment-method	analysis
analysis<-	analysis
analysis<-,SummarizedExperiment,list-method	analysis
analyze	analyze
assert_is_valid_sumexp	assert_is_valid_sumexp
AUTONOMICS_DATASETS	AUTONOMICS_DATASETS
biplot	biplot
biplot_corrections	biplot_corrections
biplot_covariates	biplot_covariates
center	center
contrastdefs	contrastdefs
contrastdefs,SummarizedExperiment-method	contrastdefs
contrastdefs<-	contrastdefs
contrastdefs<-,SummarizedExperiment,list-method	contrastdefs
contrast_subgroup_cols	contrast_subgroup_cols
contrast_subgroup_rows	contrast_subgroup_cols
counts	counts
counts,SummarizedExperiment-method	counts
counts2cpm	counts2cpm
counts2tpm	counts2tpm
counts<-	counts
counts<-,SummarizedExperiment,matrix-method	counts
counts<-,SummarizedExperiment,NULL-method	counts
counts<-,SummarizedExperiment,numeric-method	counts
cpm	cpm
cpm,SummarizedExperiment-method	cpm
cpm2counts	counts2cpm
cpm<-	cpm
cpm<-,SummarizedExperiment,matrix-method	cpm
cpm<-,SummarizedExperiment,numeric-method	cpm
create_design	create_design
create_sfile	create_sfile
default_formula	default_formula
default_sfile	default_sfile
default_subgroupvar	default_formula
download_data	download_data
download_gtf	download_gtf
dt2mat	dt2mat
exp2	log2transform
explore_imputations	explore_imputations
explore_transformations	explore_transformations
extract_features	extract_features
extract_rectangle	extract_rectangle
extract_rectangle.character	extract_rectangle
extract_rectangle.data.table	extract_rectangle
extract_rectangle.matrix	extract_rectangle
fdata	fdata
fdata,SummarizedExperiment-method	fdata
fdata<-	fdata
fdata<-,SummarizedExperiment,data.frame-method	fdata
filter_exprs_replicated_in_some_subgroup	filter_exprs_replicated_in_some_subgroup
filter_features	filter_features
filter_medoid	filter_medoid
filter_replicated	filter_replicated
filter_samples	filter_samples
fit_limma	fit_limma
fit_lm	fit_limma
fit_lme	fit_limma
fit_lmer	fit_limma
fit_wilcoxon	fit_limma
flevels	flevels
fnames	fnames
fnames,SummarizedExperiment-method	fnames
fnames<-	fnames
fnames<-,SummarizedExperiment,character-method	fnames
formula2str	formula2str
fvalues	fvalues
fvars	fvars
fvars,SummarizedExperiment-method	fvars
fvars<-	fvars
fvars<-,SummarizedExperiment,character-method	fvars
guess_maxquant_quantity	guess_maxquant_quantity
guess_maxquant_quantity.character	guess_maxquant_quantity
guess_maxquant_quantity.data.frame	guess_maxquant_quantity
guess_maxquant_quantity.SummarizedExperiment	guess_maxquant_quantity
guess_sep	guess_sep
guess_sep.character	guess_sep
guess_sep.factor	guess_sep
guess_sep.SummarizedExperiment	guess_sep
halfnormimpute	halfnormimpute
impute_systematic_nondetects	impute_systematic_nondetects
inf_to_na	zero_to_na
invert	invert
invert.character	invert
invert.SummarizedExperiment	invert
invnorm	log2transform
is_imputed	is_imputed
is_imputed,SummarizedExperiment-method	is_imputed
is_imputed<-	is_imputed
is_imputed<-,SummarizedExperiment,matrix-method	is_imputed
is_imputed<-,SummarizedExperiment,NULL-method	is_imputed
is_sig	is_sig
lda	pca
limma	limma
limma,SummarizedExperiment-method	limma
limma<-	limma
limma<-,SummarizedExperiment,array-method	limma
limma<-,SummarizedExperiment,NULL-method	limma
log2counts	log2counts
log2counts,SummarizedExperiment-method	log2counts
log2counts<-	log2counts
log2counts<-,SummarizedExperiment,matrix-method	log2counts
log2counts<-,SummarizedExperiment,numeric-method	log2counts
log2countsratios	log2countsratios
log2countsratios,SummarizedExperiment-method	log2countsratios
log2countsratios<-	log2countsratios
log2countsratios<-,SummarizedExperiment,matrix-method	log2countsratios
log2countsratios<-,SummarizedExperiment,numeric-method	log2countsratios
log2cpm	log2cpm
log2cpm,SummarizedExperiment-method	log2cpm
log2cpm<-	log2cpm
log2cpm<-,SummarizedExperiment,matrix-method	log2cpm
log2cpm<-,SummarizedExperiment,numeric-method	log2cpm
log2cpmratios	log2cpmratios
log2cpmratios,SummarizedExperiment-method	log2cpmratios
log2cpmratios<-	log2cpmratios
log2cpmratios<-,SummarizedExperiment,matrix-method	log2cpmratios
log2cpmratios<-,SummarizedExperiment,numeric-method	log2cpmratios
log2tpm	log2tpm
log2tpm,SummarizedExperiment-method	log2tpm
log2tpm<-	log2tpm
log2tpm<-,SummarizedExperiment,matrix-method	log2tpm
log2tpm<-,SummarizedExperiment,numeric-method	log2tpm
log2tpmratios	log2tpmratios
log2tpmratios,SummarizedExperiment-method	log2tpmratios
log2tpmratios<-	log2tpmratios
log2tpmratios<-,SummarizedExperiment,matrix-method	log2tpmratios
log2tpmratios<-,SummarizedExperiment,numeric-method	log2tpmratios
log2transform	log2transform
make_volcano_dt	make_volcano_dt
mat2dt	dt2mat
matrix2sumexp	matrix2sumexp
MAXQUANT_PATTERNS_PEPCOUNTS	MAXQUANT_PATTERNS_PEPCOUNTS
MAXQUANT_PATTERNS_QUANTITY	MAXQUANT_PATTERNS_QUANTITY
merge_fdata	merge_sdata
merge_ffile	merge_sfile
merge_sdata	merge_sdata
merge_sfile	merge_sfile
message_df	message_df
minusinf_to_na	zero_to_na
nan_to_na	zero_to_na
na_to_zero	zero_to_na
nfactors	split_extract
normimpute	halfnormimpute
occupancies	occupancies
occupancies,SummarizedExperiment-method	occupancies
occupancies<-	occupancies
occupancies<-,SummarizedExperiment,matrix-method	occupancies
occupancies<-,SummarizedExperiment,numeric-method	occupancies
pca	pca
plot_biplot	biplot
plot_boxplots	plot_boxplots
plot_contrastogram	plot_contrastogram
plot_corrections	biplot_corrections
plot_covariates	biplot_covariates
plot_data	plot_data
plot_densities	plot_densities
plot_detections	plot_detections
plot_detects	plot_detections
plot_features	plot_features
plot_feature_boxplots	plot_boxplots
plot_feature_densities	plot_densities
plot_feature_profiles	plot_features
plot_feature_violins	plot_violins
plot_quantifications	plot_detections
plot_sample_boxplots	plot_boxplots
plot_sample_densities	plot_densities
plot_sample_violins	plot_violins
plot_subgroup_boxplots	plot_boxplots
plot_subgroup_violins	plot_violins
plot_summarized_detections	plot_detections
plot_venn	plot_venn
plot_violins	plot_violins
plot_volcano	plot_volcano
pls	pca
preprocess_rnaseq_counts	preprocess_rnaseq_counts
proteingroups	proteingroups
proteingroups,SummarizedExperiment-method	proteingroups
proteingroups<-	proteingroups
proteingroups<-,SummarizedExperiment,matrix-method	proteingroups
proteingroups<-,SummarizedExperiment,numeric-method	proteingroups
quantnorm	log2transform
read_affymetrix	read_affymetrix
read_metabolon	read_metabolon
read_phosphosites	read_proteingroups
read_proteingroups	read_proteingroups
read_rectangles	read_rectangles
read_rnaseq_bams	read_rnaseq_counts
read_rnaseq_counts	read_rnaseq_counts
read_somascan	read_somascan
rm_singleton_samples	rm_singleton_samples
sampleid_values	svalues
scaledlibsizes	scaledlibsizes
sdata	sdata
sdata,MultiAssayExperiment-method	sdata
sdata,SummarizedExperiment-method	sdata
sdata<-	sdata
sdata<-,MultiAssayExperiment,data.frame-method	sdata
sdata<-,MultiAssayExperiment,DataFrame-method	sdata
sdata<-,SummarizedExperiment,data.frame-method	sdata
sdata<-,SummarizedExperiment,DataFrame-method	sdata
slevels	slevels
sma	pca
snames	snames
snames,SummarizedExperiment-method	snames
snames<-	snames
snames<-,SummarizedExperiment,character-method	snames
split_by_svar	split_by_svar
split_extract	split_extract
standardize_maxquant_snames	standardize_maxquant_snames
standardize_maxquant_snames.character	standardize_maxquant_snames
standardize_maxquant_snames.SummarizedExperiment	standardize_maxquant_snames
subgroup_array	subgroup_matrix
subgroup_levels	slevels
subgroup_matrix	subgroup_matrix
subgroup_values	svalues
subtract_baseline	subtract_baseline
subtract_differences	subtract_baseline
subtract_pairs	subtract_baseline
sumexp2mae	sumexp2mae
sumexp_to_long_dt	sumexp_to_long_dt
sumexp_to_subrep_dt	sumexp_to_long_dt
sumexp_to_wide_dt	sumexp_to_long_dt
summarize_fit	summarize_fit
svalues	svalues
svalues<-	svalues
svalues<-,SummarizedExperiment,character-method	svalues
svars	svars
svars,MultiAssayExperiment-method	svars
svars,SummarizedExperiment-method	svars
svars<-	svars
svars<-,MultiAssayExperiment,character-method	svars
svars<-,SummarizedExperiment,character-method	svars
TESTS	TESTS
tpm	tpm
tpm,SummarizedExperiment-method	tpm
tpm<-	tpm
tpm<-,SummarizedExperiment,matrix-method	tpm
tpm<-,SummarizedExperiment,numeric-method	tpm
translate	halfnormimpute
values	values
values,SummarizedExperiment-method	values
values<-	values
values<-,SummarizedExperiment,matrix-method	values
values<-,SummarizedExperiment,numeric-method	values
venn_detects	venn_detects
weights	weights
weights,SummarizedExperiment-method	weights
weights<-	weights
weights<-,SummarizedExperiment,matrix-method	weights
weights<-,SummarizedExperiment,NULL-method	weights
weights<-,SummarizedExperiment,numeric-method	weights
zeroimpute	halfnormimpute
zero_to_na	zero_to_na
zscore	log2transform
