%<>%	reexports
%>%	reexports
.extract_effectsize_features	extract_coef_features
.extract_fdr_features	extract_coef_features
.extract_n_features	extract_coef_features
.extract_p_features	extract_coef_features
.extract_sign_features	extract_coef_features
.fit_limma	fit
.merge	dot-merge
.plot_survival	dot-plot_survival
.read_compounddiscoverer	dot-read_compounddiscoverer
.read_diann_precursors	read_diann_proteingroups
.read_diann_proteingroups	read_diann_proteingroups
.read_maxquant_phosphosites	dot-read_maxquant_proteingroups
.read_maxquant_proteingroups	dot-read_maxquant_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
ABBREV_TO_ORGNAME	TAXON_TO_ORGNAME
abstractvar	modelvar
abstractvar.data.table	modelvar
abstractvar.SummarizedExperiment	modelvar
abstractvec	modelvar
abstractvec.data.table	modelvar
abstractvec.SummarizedExperiment	modelvar
abstract_fit	abstract_fit
add_adjusted_pvalues	add_adjusted_pvalues
add_assay_means	add_assay_means
add_facetvars	add_facetvars
add_opentargets_by_uniprot	add_opentargets_by_uniprot
add_psp	add_psp
add_smiles	add_smiles
altenrich	altenrich
analysis	analysis
analysis,SummarizedExperiment-method	analysis
analysis<-	analysis
analysis<-,SummarizedExperiment,list-method	analysis
analyze	analyze
annotate_maxquant	annotate_maxquant
annotate_uniprot_rest	annotate_uniprot_rest
assert_compounddiscoverer_output	is_diann_report
assert_correlation_matrix	is_correlation_matrix
assert_diann_report	is_diann_report
assert_fastadt	is_fastadt
assert_fragpipe_tsv	is_diann_report
assert_is_fraction	is_fraction
assert_is_valid_sumexp	assert_is_valid_sumexp
assert_maxquant_phosphosites	is_diann_report
assert_maxquant_proteingroups	is_diann_report
assert_positive_number	is_positive_number
assert_scalar_subset	is_scalar_subset
assert_valid_formula	is_valid_formula
assert_weakly_positive_number	is_positive_number
AUTONOMICS_DATASETS	AUTONOMICS_DATASETS
beta	X
bin	bin
bin.character	bin
bin.factor	bin
bin.logical	bin
bin.numeric	bin
bin.SummarizedExperiment	bin
biplot	biplot
biplot_corrections	biplot_corrections
biplot_covariates	biplot_covariates
block2lme	block2lme
block2lme.character	block2lme
block2lme.formula	block2lme
block2lme.list	block2lme
block_vars	block2lme
cbind_imputed	split_samples
center	center
code	code
code.data.table	code
code.factor	code
code_control	code
code_deviation	code
code_deviation_first	code
code_diff	code
code_diff_forward	code
code_helmert	code
code_helmert_forward	code
coefs	coefs
coefs.data.table	coefs
coefs.factor	coefs
coefs.SummarizedExperiment	coefs
collapsed_entrezg_to_symbol	collapsed_entrezg_to_symbol
collapse_in	count_in
collapse_in.character	count_in
collapse_in.factor	count_in
collapse_in.list	count_in
COMPOUNDDISCOVERER_PATTERNS	COMPOUNDDISCOVERER_PATTERNS
CONTAMINANTSURL	CONTAMINANTSURL
contr.diff	code
contr.treatment.explicit	code
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
count_in	count_in
count_in.character	count_in
count_in.factor	count_in
count_in.list	count_in
count_out	count_in
count_out.character	count_in
count_out.factor	count_in
count_out.list	count_in
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_design.data.table	create_design
create_design.SummarizedExperiment	create_design
data.table	reexports
DATADIR	download_data
default_coefs	default_coefs
default_coefs.data.table	default_coefs
default_coefs.SummarizedExperiment	default_coefs
default_formula	default_formula
default_geom	default_geom
default_sfile	default_sfile
default_subgroupvar	default_formula
demultiplex	demultiplex
dequantify	dequantify
dequantify_compounddiscoverer	dequantify_compounddiscoverer
downfeatures	modelvar
download_contaminants	download_contaminants
download_data	download_data
download_gtf	download_gtf
download_mcclain21	download_mcclain21
download_tcga_example	download_tcga_example
dt2mat	dt2mat
effectdt	modelvar
effectmat	modelvar
effectsizemat	modelvar
effectvar	modelvar
effectvec	modelvar
enrichment	enrichment
ens2org	taxon2org
entrezg_to_symbol	entrezg_to_symbol
EXISTENCE_TO_NUMBER	TAXON_TO_ORGNAME
exp2	log2transform
explore_transformations	explore_transformations
extract	reexports
extract_coef_features	extract_coef_features
extract_rectangle	extract_rectangle
extract_rectangle.character	extract_rectangle
extract_rectangle.data.table	extract_rectangle
extract_rectangle.matrix	extract_rectangle
factor2logical	logical2factor
fcluster	fcluster
fcor	fcor
fdata	fdata
fdata,SummarizedExperiment-method	fdata
fdata<-	fdata
fdata<-,SummarizedExperiment,data.frame-method	fdata
fdist	fcor
fdr2p	fdr2p
fdrmat	modelvar
fdrvar	modelvar
fdrvec	modelvar
fdt	fdata
fdt,SummarizedExperiment-method	fdata
fdt<-	fdata
fdt<-,SummarizedExperiment,data.table-method	fdata
filter_exprs_replicated_in_some_subgroup	filter_exprs_replicated_in_some_subgroup
filter_features	filter_features
filter_medoid	filter_medoid
filter_samples	filter_samples
fit	fit
fitcoefs	fitcoefs
fitdt	fitvars
fits	fits
fits.data.table	fits
fits.SummarizedExperiment	fits
FITSEP	FITSEP
fitvars	fitvars
fit_limma	fit
fit_lm	fit_lmx
fit_lme	fit_lmx
fit_lmer	fit_lmx
fit_lmx	fit_lmx
fit_survival	dot-plot_survival
fit_wilcoxon	fit
fix_xlgenes	fix_xlgenes
flevels	flevels
fnames	fnames
fnames,SummarizedExperiment-method	fnames
fnames<-	fnames
fnames<-,SummarizedExperiment,character-method	fnames
formula2lm	block2lme
formula2lmer	block2lme
formula2str	formula2str
fscale	log2transform
ftype	ftype
fvalues	fvalues
fvars	fvars
fvars,SummarizedExperiment-method	fvars
fvars<-	fvars
fvars<-,SummarizedExperiment,character-method	fvars
genome_to_orgdb	genome_to_orgdb
group_by_level	group_by_level
group_by_level.character	group_by_level
group_by_level.data.table	group_by_level
group_by_level.factor	group_by_level
guess_compounddiscoverer_quantity	guess_compounddiscoverer_quantity
guess_fitsep	guess_fitsep
guess_fitsep.data.table	guess_fitsep
guess_fitsep.SummarizedExperiment	guess_fitsep
guess_maxquant_quantity	guess_maxquant_quantity
guess_sep	guess_sep
guess_sep.character	guess_sep
guess_sep.factor	guess_sep
guess_sep.numeric	guess_sep
guess_sep.SummarizedExperiment	guess_sep
has_multiple_levels	has_multiple_levels
has_multiple_levels.character	has_multiple_levels
has_multiple_levels.data.table	has_multiple_levels
has_multiple_levels.factor	has_multiple_levels
has_multiple_levels.numeric	has_multiple_levels
has_multiple_levels.SummarizedExperiment	has_multiple_levels
hdlproteins	hdlproteins
impute	impute
impute.matrix	impute
impute.numeric	impute
impute.SummarizedExperiment	impute
inf_to_na	zero_to_na
invert_subgroups	invert_subgroups
invnorm	log2transform
is_collapsed_subset	is_collapsed_subset
is_compounddiscoverer_output	is_diann_report
is_correlation_matrix	is_correlation_matrix
is_diann_report	is_diann_report
is_fastadt	is_fastadt
is_file	is_file
is_fraction	is_fraction
is_fragpipe_tsv	is_diann_report
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_maxquant_phosphosites	is_diann_report
is_maxquant_proteingroups	is_diann_report
is_positive_number	is_positive_number
is_scalar_subset	is_scalar_subset
is_sig	is_sig
is_valid_formula	is_valid_formula
is_weakly_positive_number	is_positive_number
keep_connected_blocks	keep_connected_blocks
keep_connected_features	keep_connected_features
keep_replicated_features	keep_replicated_features
label2index	label2index
lda	pca
LINMOD_ENGINES	LINMOD_ENGINES
list2mat	list2mat
list_files	list_files
loadingmat	scoremat
loadings	scoremat
log2counts	log2counts
log2counts,SummarizedExperiment-method	log2counts
log2counts<-	log2counts
log2counts<-,SummarizedExperiment,matrix-method	log2counts
log2counts<-,SummarizedExperiment,numeric-method	log2counts
log2cpm	log2cpm
log2cpm,SummarizedExperiment-method	log2cpm
log2cpm<-	log2cpm
log2cpm<-,SummarizedExperiment,matrix-method	log2cpm
log2cpm<-,SummarizedExperiment,numeric-method	log2cpm
log2diffs	log2diffs
log2diffs,SummarizedExperiment-method	log2diffs
log2diffs<-	log2diffs
log2diffs<-,SummarizedExperiment,matrix-method	log2diffs
log2diffs<-,SummarizedExperiment,numeric-method	log2diffs
log2proteins	log2proteins
log2proteins,SummarizedExperiment-method	log2proteins
log2proteins<-	log2proteins
log2proteins<-,SummarizedExperiment,matrix-method	log2proteins
log2proteins<-,SummarizedExperiment,numeric-method	log2proteins
log2sites	log2sites
log2sites,SummarizedExperiment-method	log2sites
log2sites<-	log2sites
log2sites<-,SummarizedExperiment,matrix-method	log2sites
log2sites<-,SummarizedExperiment,numeric-method	log2sites
log2tpm	log2tpm
log2tpm,SummarizedExperiment-method	log2tpm
log2tpm<-	log2tpm
log2tpm<-,SummarizedExperiment,matrix-method	log2tpm
log2tpm<-,SummarizedExperiment,numeric-method	log2tpm
log2transform	log2transform
logical2factor	logical2factor
make_alpha_palette	make_alpha_palette
make_colors	make_colors
make_volcano_dt	make_volcano_dt
map_fvalues	map_fvalues
mat2dt	dt2mat
matrix2sumexp	matrix2sumexp
MAXQUANT_PATTERNS	MAXQUANT_PATTERNS
mdsplot	fcor
merge_compounddiscoverer	merge_compounddiscoverer
merge_fdata	merge_sdata
merge_fdt	merge_sdata
merge_ffile	merge_sample_file
merge_sample_excel	merge_sample_excel
merge_sample_file	merge_sample_file
merge_sdata	merge_sdata
merge_sdt	merge_sdata
message_df	message_df
minusinf_to_na	zero_to_na
modeldt	modelvar
modeldt.data.table	modelvar
modeldt.SummarizedExperiment	modelvar
modelfeatures	modelvar
modelfeatures.data.table	modelvar
modelfeatures.SummarizedExperiment	modelvar
modelmat	modelvar
modelvar	modelvar
modelvar.data.table	modelvar
modelvar.SummarizedExperiment	modelvar
modelvec	modelvar
modelvec.data.table	modelvar
modelvec.SummarizedExperiment	modelvar
MSIGCOLLECTIONSHUMAN	MSIGCOLLECTIONSHUMAN
MSIGCOLLECTIONSMOUSE	MSIGCOLLECTIONSHUMAN
MSIGDIR	MSIGDIR
nan_to_na	zero_to_na
na_to_string	zero_to_na
na_to_zero	zero_to_na
nfactors	split_extract_fixed
no_nas	systematic_nas
OPENTARGETSDIR	OPENTARGETSDIR
opls	pca
order_on_effect	order_on_p
order_on_p	order_on_p
parse_maxquant_hdrs	read_uniprotdt
pca	pca
pdt	modelvar
percentiles	percentiles
pg_to_canonical	pg_to_canonical
pg_to_isoforms	pg_to_canonical
plot_contrastogram	plot_contrastogram
plot_contrast_venn	plot_contrast_venn
plot_data	plot_data
plot_densities	plot_densities
plot_design	plot_design
plot_detections	plot_sample_nas
plot_exprs	plot_exprs
plot_exprs_per_coef	plot_exprs_per_coef
plot_feature_boxplots	plot_exprs
plot_feature_densities	plot_densities
plot_feature_violins	plot_violins
plot_fit_summary	plot_fit_summary
plot_heatmap	plot_heatmap
plot_matrix	plot_matrix
plot_sample_boxplots	plot_exprs
plot_sample_densities	plot_densities
plot_sample_nas	plot_sample_nas
plot_sample_violins	plot_violins
plot_subgroup_nas	plot_sample_nas
plot_subgroup_points	plot_subgroup_points
plot_subgroup_violins	plot_violins
plot_summarized_detections	plot_sample_nas
plot_summary	plot_summary
plot_survival	dot-plot_survival
plot_venn	plot_venn
plot_venn_heatmap	plot_venn_heatmap
plot_violins	plot_violins
plot_volcano	plot_volcano
pls	pca
pmat	modelvar
PPATTERN	FITSEP
PRECURSOR_QUANTITY	PRECURSOR_QUANTITY
preprocess_rnaseq_counts	preprocess_rnaseq_counts
pull_columns	pull_columns
pvar	modelvar
pvec	modelvar
quantnorm	log2transform
random_nas	systematic_nas
read_affymetrix	read_affymetrix
read_compounddiscoverer	read_compounddiscoverer
read_contaminantdt	read_uniprotdt
read_contaminants	read_contaminants
read_diann	read_diann_proteingroups
read_diann_proteingroups	read_diann_proteingroups
read_fragpipe	read_fragpipe
read_maxquant_phosphosites	read_maxquant_phosphosites
read_maxquant_proteingroups	read_maxquant_proteingroups
read_metabolon	read_metabolon
read_msigdt	read_msigdt
read_olink	read_olink
read_phosphosites	read_maxquant_phosphosites
read_proteingroups	read_maxquant_proteingroups
read_rectangles	read_rectangles
read_rnaseq_bams	read_rnaseq_counts
read_rnaseq_counts	read_rnaseq_counts
read_salmon	read_salmon
read_somascan	read_somascan
read_uniprotdt	read_uniprotdt
recollapse	uncollapse
reexports	reexports
reset_fit	reset_fit
REVIEWED_TO_NUMBER	TAXON_TO_ORGNAME
rm_diann_contaminants	rm_diann_contaminants
rm_missing_in_all_samples	rm_missing_in_some_samples
rm_missing_in_some_samples	rm_missing_in_some_samples
rm_singleton_samples	rm_unmatched_samples
rm_unmatched_samples	rm_unmatched_samples
sampleid_values	svalues
scaledlibsizes	scaledlibsizes
scor	fcor
scoremat	scoremat
scores	scoremat
sdata	fdata
sdata,SummarizedExperiment-method	fdata
sdata<-	fdata
sdata<-,SummarizedExperiment,data.frame-method	fdata
sdata<-,SummarizedExperiment,DataFrame-method	fdata
sdist	fcor
sdt	fdata
sdt,SummarizedExperiment-method	fdata
sdt<-	fdata
sdt<-,SummarizedExperiment,data.table-method	fdata
slevels	slevels
sma	pca
snames	snames
snames,SummarizedExperiment-method	snames
snames<-	snames
snames<-,SummarizedExperiment,character-method	snames
split_extract	split_extract_fixed
split_extract_fixed	split_extract_fixed
split_extract_regex	split_extract_fixed
split_features	split_samples
split_samples	split_samples
spls	pca
sscale	log2transform
stri_any_regex	stri_any_regex
stri_detect_fixed_in_collapsed	stri_detect_fixed_in_collapsed
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
sumexplist_to_longdt	sumexplist_to_longdt
sumexp_to_longdt	sumexp_to_longdt
sumexp_to_subrep_dt	sumexp_to_longdt
sumexp_to_tsv	sumexp_to_tsv
sumexp_to_widedt	sumexp_to_longdt
summarize_fit	summarize_fit
summarize_fit.data.table	summarize_fit
summarize_fit.SummarizedExperiment	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
systematic_nas	systematic_nas
tag_features	tag_features
tag_hdlproteins	tag_hdlproteins
taxon2org	taxon2org
TAXON_TO_ORGNAME	TAXON_TO_ORGNAME
tdt	modelvar
TESTS	TESTS
tmat	modelvar
tpm	tpm
tpm,SummarizedExperiment-method	tpm
tpm<-	tpm
tpm<-,SummarizedExperiment,matrix-method	tpm
tpm<-,SummarizedExperiment,numeric-method	tpm
tvar	modelvar
tvec	modelvar
twofactor_sumexp	twofactor_sumexp
uncollapse	uncollapse
upfeatures	modelvar
values	values
values,SummarizedExperiment-method	values
values<-	values
values<-,SummarizedExperiment,matrix-method	values
values<-,SummarizedExperiment,numeric-method	values
varlevels_dont_clash	varlevels_dont_clash
varlevels_dont_clash.data.table	varlevels_dont_clash
varlevels_dont_clash.SummarizedExperiment	varlevels_dont_clash
venn_detects	venn_detects
vsn	log2transform
weights	weights
weights,SummarizedExperiment-method	weights
weights<-	weights
weights<-,SummarizedExperiment,matrix-method	weights
weights<-,SummarizedExperiment,NULL-method	weights
weights<-,SummarizedExperiment,numeric-method	weights
write_ods	write_xl
write_xl	write_xl
X	X
zero_to_na	zero_to_na
zscore	log2transform
