abstract	abstract
adjacent	propr
aldex.cor	aldex.cor
aldex2propr	aldex2propr
alphaTheta	alphaTheta
alphaThetaW_old	alphaThetaW_old
alphaTheta_old	alphaTheta_old
bokeh	visualize
bowtie	propd
bucket	visualize
calculateFDR	calculateFDR
calculateFDR_old	calculateFDR_old
calculateTheta	calculateTheta
calculateThetaW_old	calculateThetaW_old
calculateTheta_old	calculateTheta_old
caneToad.counts	caneToad.counts
caneToad.groups	caneToad.groups
corr	proportionality
cytescape	visualize
decomposed	propd
dendroCheck	dendroCheck
dendrogram	visualize
differentialCheck	differentialCheck
gemini	propd
geyser	propd
ggdend	ggdend
initialize,propr-method	proportionality
ivar2index	ivar2index
lr2cor	lr2cor
mail	mail
marg.abs	marg.abs
migraph	migraph
migraph.add	migraph
migraph.clean	migraph
migraph.color	migraph
multiplot	multiplot
packageCheck	packageCheck
pals	pals
pca	visualize
pd.d	pd.d
pd.e	pd.e
perb	proportionality
permuteTheta	permuteTheta
permuteTheta_false	permuteTheta_false
permuteTheta_naive	permuteTheta_naive
permuteTheta_old	permuteTheta_old
permuteTheta_prime	permuteTheta_prime
phis	proportionality
phit	proportionality
plot,propd,missing-method	propd
plot,propr,missing-method	propr
plotCheck	plotCheck
prism	visualize
progress	progress
promptCheck	promptCheck
prop2prob	prop2prob
propd	propd
propd-class	propd
propd2propr	propd
proportionality	proportionality
propr	propr
propr-class	propr
proprALR	proprALR
proprCLR	proprCLR
proprPairs	proprPairs
proprPerb	proprPerb
proprPhit	proprPhit
proprSym	proprSym
proprTri	proprTri
proprVLR	proprVLR
ratios	ratios
setActive	propd
setDisjointed	propd
setEmergent	propd
shale	propd
show,propd-method	propd
show,propr-method	propr
simplify	propr
slate	visualize
slice	propd
smear	visualize
snapshot	visualize
subset,propr-method	propr
top.counts	top.counts
top.lr	top.lr
updateCutoffs	propd
updateF	propd
visualize	visualize
[,propr,ANY,ANY-method	propr
[,propr-method	propr
