aldex2propr	aldex2propr
as_safe_matrix	as_safe_matrix
calculate_theta	calculate_theta
compute_iqlr	compute_iqlr
countValuesBeyondThreshold	countValuesBeyondThreshold
getAdjacencyFDR	getAdjacencyFDR
getAdjacencyFstat	getAdjacencyFstat
getCutoffFDR	getCutoffFDR
getCutoffFstat	getCutoffFstat
getFdrRandcounts.propd.parallel	getFdrRandcounts.propd.parallel
getFdrRandcounts.propd.run	getFdrRandcounts.propd.run
getFdrRandcounts.propr.parallel	getFdrRandcounts.propr.parallel
getFdrRandcounts.propr.run	getFdrRandcounts.propr.run
getMatrix	getMatrix
getMovingAverage	getMovingAverage
getPermutedTheta	getPermutedTheta
getPermutedThetaMod	getPermutedThetaMod
getRatios	getRatios
getResults	getResults
getSignificantResultsFDR	getSignificantResultsFDR
getSignificantResultsFDR.propd	getSignificantResultsFDR
getSignificantResultsFDR.propr	getSignificantResultsFDR
getSignificantResultsFstat	getSignificantResultsFstat
index_reference	index_reference
logratio	logratio
logratio_without_alpha	logratio_without_alpha
logratio_with_alpha	logratio_with_alpha
lrv_with_shrinkage	lrv_with_shrinkage
marg.abs	marg.abs
packageCheck	packageCheck
pcor.bshrink	pcor.bshrink
progress	progress
propd	propd
propd-class	propd
propr	propr
propr-class	propr
ratios	ratios
results_to_matrix	results_to_matrix
runGraflex	runGraflex
runNormalization	runNormalization
runPostHoc	runPostHoc
search_tree	search_tree
selectRatios	selectRatios
selectReference	selectReference
setActive	propd
setDisjointed	propd
setEmergent	propd
show,propd-method	propd
show,propr-method	propr
simple_zero_replacement	simple_zero_replacement
updateCutoffs	updateCutoffs
updateCutoffs.propd	updateCutoffs
updateCutoffs.propr	updateCutoffs
updateF	propd
updatePermutes	updatePermutes
