Reference

All functions
DEprot-class	DEprot class
DEprot-dollar-methods	Slot access for DEprot classes
DEprot.PCA-class	DEprot.PCA class
DEprot.PCoA-class	DEprot.PCoA class
DEprot.RMSE-class	DEprot.RMSE class
DEprot.SAINTq-class	DEprot.SAINTq class
DEprot.analyses-class	DEprot.analyses class
DEprot.contrast.heatmap-class	DEprot.contrast.heatmap class
DEprot.correlation-class	DEprot.correlation class
DEprot.counts.heatmap-class	DEprot.counts.heatmap class
DEprot.enrichResult-class	DEprot.enrichResult class
DEprot.missingness-class	DEprot.missingness class
DEprot.normality-class	DEprot.normality class
DEprot.outliers-class	DEprot.outliers class
DEprot.power-class	DEprot.power class
DEprot.pvalues-class	DEprot.pvalues class
DEprot.timecourse-class	DEprot.timecourse class
DEprot.timecourse.enrichment-class	DEprot.timecourse.enrichment class
DEprot.upset-class	DEprot.upset class
NES.plot()	NES.plot
SAINTq()	SAINTq
add.protein.info()	add.protein.info
affinity.propagation()	affinity.propagation
analyze.timecourse()	analyze.timecourse
as.MSnSet()	as.MSnSet
as.QFeatures()	as.QFeatures
as.SummarizedExperiment()	as.SummarizedExperiment
check.normality()	check.normality
check.pvalues()	check.pvalues
combine.enrichments()	combine.enrichments
compare.imp.methods()	compare.imp.methods
compare.ranking()	compare.ranking
contrast.LFQ()	contrast.LFQ
contrast.scatter()	contrast.scatter
corum_v4.1	CORUM version 4.1
corum_v5.0	CORUM version 5.0
detect.outliers()	detect.outliers
diff.analyses()	diff.analyses
diff.analyses.limma()	diff.analyses.limma
diff.analyses.proDA()	diff.analyses.proDA
diff.analyses.prolfqua()	diff.analyses.prolfqua
divergent.enrichment()	divergent.enrichment
dpo.imputed.counts	Imputed proteomics (LFQ) data
estimate.power()	estimate.power
export.analyses()	export.analyses
export.external()	export.external
export.report()	export.report
expression.boxplot()	expression.boxplot
filter.proteins()	filter.proteins
filter.samples()	filter.samples
geneset.enrichment()	geneset.enrichment
get.metadata()	get.metadata
get.protein.info()	get.protein.info
get.results()	get.results
get.timecourse.results()	get.timecourse.results
harmonize.batches()	harmonize.batches
heatmap.contrasts()	heatmap.contrasts
heatmap.counts()	heatmap.counts
heatmap.timecourse()	heatmap.timecourse
identify.distribution()	identify.distribution
import.external()	import.external
import.msstats()	import.msstats
impute.counts()	impute.counts
jaccardSim()	jaccardSim
load.counts2()	load.counts2
missingness.diagnostic()	missingness.diagnostic
normalize.counts()	normalize.counts
perform.PCA()	perform.PCA
perform.PCoA()	perform.PCoA
plot(<DEprot.power>,<ANY>)	DEprot.power plot-method
plot(<DEprot.timecourse>,<ANY>)	DEprot.timecourse plot-method
plot(<DEprot.timecourse.enrichment>,<ANY>)	DEprot.timecourse.enrichment plot-method
plot.GSEA()	plot.GSEA
plot.MA()	plot.MA
plot.PC.biplot()	plot.PC.biplot
plot.PC.cumulative()	plot.PC.cumulative
plot.PC.scatter.123()	plot.PC.scatter.123
plot.PC.scatter()	plot.PC.scatter
plot.PCoA.biplot()	plot.PCoA.biplot
plot.PCoA.cumulative()	plot.PCoA.cumulative
plot.PCoA.scatter.123()	plot.PCoA.scatter.123
plot.PCoA.scatter()	plot.PCoA.scatter
plot.correlation.heatmap()	plot.correlation.heatmap
plot.counts()	plot.counts
plot.timecourse.profiles()	plot.timecourse.profiles
plot.timecourse.protein()	plot.timecourse.protein
plot.upset()	plot.upset
plot.volcano()	plot.volcano
protein.summary()	protein.summary
randomize.missing.values()	randomize.missing.values
rank.timecourse()	rank.timecourse
reapply.thresholds()	reapply.thresholds
remove.undetected.proteins()	remove.undetected.proteins
rename.samples()	rename.samples
rescale.bait()	rescale.bait
rime.dpo	Imputed RIME (LFQ) data
rime.saintq	SAINTq results for RIME
sample.config	Example of metadata table
show(<DEprot>)	DEprot show-method
show(<DEprot.PCA>)	DEprot.PCA show-method
show(<DEprot.PCoA>)	DEprot.PCoA show-method
show(<DEprot.RMSE>)	DEprot.RMSE show-method
show(<DEprot.SAINTq>)	DEprot.SAINTq show-method
show(<DEprot.analyses>)	DEprot.analyses show-method
show(<DEprot.contrast.heatmap>)	DEprot.contrast.heatmap show-method
show(<DEprot.correlation>)	DEprot.correlation show-method
show(<DEprot.counts.heatmap>)	DEprot.counts.heatmap show-method
show(<DEprot.enrichResult>)	DEprot.enrichResult show-method
show(<DEprot.missingness>)	DEprot.missingness show-method
show(<DEprot.normality>)	DEprot.normality show-method
show(<DEprot.outliers>)	DEprot.outliers show-method
show(<DEprot.power>)	DEprot.power show-method
show(<DEprot.pvalues>)	DEprot.pvalues show-method
show(<DEprot.timecourse>)	DEprot.timecourse show-method
show(<DEprot.timecourse.enrichment>)	DEprot.timecourse.enrichment show-method
show(<DEprot.upset>)	DEprot.upset show-method
simplify.enrichment()	simplify.enrichment
summary(<DEprot.RMSE>)	DEprot.RMSE summary-method
summary(<DEprot.SAINTq>)	DEprot.SAINTq summary-method
summary(<DEprot.analyses>)	DEprot.analyses summary-method
summary(<DEprot.missingness>)	DEprot.missingness summary-method
summary(<DEprot.timecourse>)	DEprot.timecourse summary-method
test.toolbox	Test toolbox
timecourse.enrichment()	timecourse.enrichment
unimputed.counts	Unimputed proteomics (LFQ) data