%<>%	reexports
%>%	reexports
.coxph	dot-coxph
.densities	densities
.extract_effectsize_features	extract_contrast_features
.extract_fdr_features	extract_contrast_features
.extract_n_features	extract_contrast_features
.extract_p_features	extract_contrast_features
.fit_survival	fit_survival
.logrank	dot-coxph
.merge	dot-merge
.read_compounddiscoverer	dot-read_compounddiscoverer
.read_compounddiscoverer_masslist	dot-read_compounddiscoverer_masslist
.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
.survdiff	dot-coxph
ABBREV_TO_ORGNAME	TAXON_TO_ORGNAME
abind	sbind
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_adjusted_pvalues.data.table	add_adjusted_pvalues
add_adjusted_pvalues.NULL	add_adjusted_pvalues
add_adjusted_pvalues.SummarizedExperiment	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
all_non_numeric	all_non_numeric
altenrich	altenrich
analysis	analysis
analysis,SummarizedExperiment-method	analysis
analysis<-	analysis
analysis<-,SummarizedExperiment,list-method	analysis
analyze	analyze
annotate_compounddiscoverer	annotate_compounddiscoverer
annotate_maxquant	annotate_maxquant
annotate_uniprot_rest	annotate_uniprot_rest
assert_character_matrix	is_character_matrix
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
awblinmod	awblinmod
awblinmod_limma	awblinmod
awblinmod_lm	awblinmod
awblinmod_lme	awblinmod
awblinmod_lmer	awblinmod
beta	X
bin	factorize
bin.character	factorize
bin.factor	factorize
bin.logical	factorize
bin.matrix	factorize
bin.numeric	factorize
bin.SummarizedExperiment	factorize
bin_assay	factorize
biplot	biplot
biplot_corrections	biplot_corrections
biplot_covariates	biplot_covariates
biplot_transforms	explore-transforms
biplot_transforms_assays	explore-transforms
block2limma	block2limma
block2limma.character	block2limma
block2limma.formula	block2limma
block2limma.list	block2limma
block2limma.NULL	block2limma
block2lm	block2lm
block2lm.character	block2lm
block2lm.formula	block2lm
block2lm.list	block2lm
block2lm.NULL	block2lm
block2lme	block2lme
block2lme.character	block2lme
block2lme.formula	block2lme
block2lme.list	block2lme
block2lmer	block2lmer
block2lmer.character	block2lmer
block2lmer.formula	block2lmer
block2lmer.list	block2lmer
block_has_two_levels	block_has_two_levels
cbind_imputed	split_samples
center	center
center_mean	center
center_median	center
code	code
code.character	code
code.data.table	code
code.factor	code
code.logical	code
code.numeric	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	fits
coefs.data.table	fits
coefs.factor	fits
coefs.NULL	fits
coefs.SummarizedExperiment	fits
coefs_estimable	pvalues_estimable
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
contr.diff	code
contr.treatment.explicit	code
contrastdt	contrastdt
contrast_coefs	model_coefs
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
defaultmsigfile	defaultmsigfile
default_formula	default_formula
default_geom	default_geom
default_sfile	default_sfile
demultiplex	demultiplex
densities	densities
dequantify	dequantify
dequantify_compounddiscoverer	dequantify_compounddiscoverer
DIMREDENGINES	DIMREDENGINES
DIMREDSUPER	DIMREDENGINES
DIMREDUN	DIMREDENGINES
downfeatures	modelvar
download_data	download_data
download_gtf	download_gtf
download_mcclain21	download_mcclain21
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
exp2transform	log2transform
extract	reexports
extract_contrast_features	extract_contrast_features
extract_rectangle	extract_rectangle
extract_rectangle.character	extract_rectangle
extract_rectangle.data.table	extract_rectangle
extract_rectangle.matrix	extract_rectangle
factor.vars	factor.vars
factor.vars,formula,data.table-method	factor.vars
factor.vars,formula,SummarizedExperiment-method	factor.vars
factor2logical	logical2factor
factorize	factorize
factorize.character	factorize
factorize.factor	factorize
factorize.logical	factorize
factorize.matrix	factorize
factorize.numeric	factorize
factorize.SummarizedExperiment	factorize
factorize_assay	factorize
fbind	sbind
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
fitcoefs	fits
fits	fits
fits.data.table	fits
fits.NULL	fits
fits.SummarizedExperiment	fits
fit_limma	LINMOD
fit_lm	LINMOD
fit_lme	LINMOD
fit_lmer	LINMOD
fit_survival	fit_survival
fit_wilcoxon	LINMOD
fix_xlgenes	fix_xlgenes
flevels	flevels
fnames	fnames
fnames,SummarizedExperiment-method	fnames
fnames<-	fnames
fnames<-,SummarizedExperiment,character-method	fnames
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
installed	installed
invert_subgroups	invert_subgroups
invnorm	log2transform
is_character_matrix	is_character_matrix
is_collapsed_subset	is_collapsed_subset
is_compounddiscoverer_output	is_compounddiscoverer_output
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_fragpipe_tsv
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_maxquant_phosphosites
is_maxquant_proteingroups	is_maxquant_proteingroups
is_non_numeric	all_non_numeric
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_estimable_features	keep_estimable_features
label2index	label2index
lda	pca
left.vars	factor.vars
LINMOD	LINMOD
LINMODENGINES	LINMODENGINES
linmod_limma	LINMOD
linmod_lm	LINMOD
linmod_lme	LINMOD
linmod_lmer	LINMOD
linmod_wilcoxon	LINMOD
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
mclust_breaks	mclust_breaks
mclust_parameters	overall_parameters
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
mixtools_breaks	mclust_breaks
mixtools_parameters	overall_parameters
modeldt	modelvar
modeldt.data.table	modelvar
modeldt.NULL	modelvar
modeldt.SummarizedExperiment	modelvar
modelfeatures	modelvar
modelfeatures.data.table	modelvar
modelfeatures.SummarizedExperiment	modelvar
modelmat	modelvar
modelvar	modelvar
modelvar.data.table	modelvar
modelvar.NULL	modelvar
modelvar.SummarizedExperiment	modelvar
modelvec	modelvar
modelvec.data.table	modelvar
modelvec.SummarizedExperiment	modelvar
model_coefs	model_coefs
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
object1	object1
object2	object1
OPENTARGETSDIR	OPENTARGETSDIR
opls	pca
order_on_effect	order_on_p
order_on_p	order_on_p
order_on_t	order_on_p
overall_parameters	overall_parameters
parse_maxquant_hdrs	read_uniprotdt
pca	pca
pdt	modelvar
pg_to_canonical	pg_to_canonical
pg_to_isoforms	pg_to_canonical
plot_coef_densities	plot_coef_densities
plot_contrastogram	plot_contrastogram
plot_contrast_venn	plot_contrast_venn
plot_data	plot_data
plot_densities	plot_densities
plot_densities_transforms	explore-transforms
plot_design	plot_design
plot_detections	plot_detections
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_detections
plot_sample_violins	plot_violins
plot_subgroup_nas	plot_detections
plot_subgroup_points	plot_subgroup_points
plot_subgroup_violins	plot_violins
plot_summarized_detections	plot_detections
plot_summary	plot_summary
plot_survival	fit_survival
plot_venn	plot_venn
plot_venn_heatmap	plot_venn_heatmap
plot_violins	plot_violins
plot_violins_transforms	explore-transforms
plot_volcano	plot_volcano
plot_xy_density	plot_xy_density
plot_xy_scatter	plot_xy_density
plot_x_density	plot_xy_density
plot_y_density	plot_xy_density
pls	pca
pmat	modelvar
PRECURSOR_QUANTITY	PRECURSOR_QUANTITY
preprocess_rnaseq_counts	preprocess_rnaseq_counts
prep_survival	fit_survival
pull_columns	pull_columns
pvalues_estimable	pvalues_estimable
pvar	modelvar
pvec	modelvar
quantile_breaks	mclust_breaks
quantnorm	log2transform
random_nas	systematic_nas
read_affymetrix	read_affymetrix
read_compounddiscoverer	read_compounddiscoverer
read_contaminantdt	read_uniprotdt
read_diann	read_diann_proteingroups
read_diann_pgmatrix	read_diann_phosphodiffs
read_diann_phosphodiffs	read_diann_phosphodiffs
read_diann_phosphosites	read_diann_phosphodiffs
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
right.vars	factor.vars
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
sbind	sbind
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
stepauc	stepauc
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_groupdt	sumexp_to_longdt
sumexp_to_longdt	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
survobj	survobj
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
TRANSFORMENGINES	TRANSFORMENGINES
TRANSFORMSTRICT	TRANSFORMENGINES
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
