MAST-package	MAST-package
"summary-ZlmFit",	summary-ZlmFit-method
"ZlmFit-summary"	summary-ZlmFit-method
applyFlat	applyFlat
assay,SingleCellAssay,missing-method	defaultAssay
BayesGLMlike-class	BayesGLMlike-class
bootVcov1	bootVcov1
burdenOfFiltering	mast_filter
calcZ	calcZ
cData	cData
cData,SingleCellAssay-method	cData
cData<-	cData
cData<-,SingleCellAssay-method	cData
coef,LMERlike-method	LMERlike-class
coef,ZlmFit-method	ZlmFit-class
CoefficientHypothesis	Hypothesis
colData<-,SingleCellAssay,DataFrame-method	colData-set-SingleCellAssay-DataFrame-method
collectResiduals	collectResiduals
combine,SingleCellAssay,ANY-method	cData
combine,SingleCellAssay,SingleCellAssay-method	cData
combined_residuals_hook	collectResiduals
computeEtFromCt	computeEtFromCt
condmean	freq
condSd	freq
continuous_residuals_hook	collectResiduals
convertMASTClassicToSingleCellAssay	convertMASTClassicToSingleCellAssay
defaultAssay	defaultAssay
defaultPrior	defaultPrior
deviance_residuals_hook	collectResiduals
discrete_residuals_hook	collectResiduals
dof	dof
dof,GLMlike-method	dof
Drop	Drop
ebayes	ebayes
expavg	expavg
fData	fData-methods
fData,SingleCellAssay-method	fData-methods
featureData	featureData-methods
featureData,SingleCellAssay-method	featureData-methods
filter	mast_filter
filterLowExpressedGenes	filterLowExpressedGenes
fit	fit
fit,GLMlike,missing-method	fit
fit,LMERlike,missing-method	fit
fitted_phat	collectResiduals
FluidigmAssay	FromFlatDF
freq	freq
FromFlatDF	FromFlatDF
FromMatrix	FromMatrix
getConcordance	getConcordance
getLogFC	logFC
getrc	getConcordance
getss	getConcordance
getwellKey	getwellKey
getwellKey,SingleCellAssay-method	getwellKey
getwss	getConcordance
GLMlike-class	GLMlike-class
gseaAfterBoot	gseaAfterBoot
GSEATests-class	GSEATests-class
hushWarning	hushWarning
Hypothesis	Hypothesis
impute	impute
influence.bayesglm	influence.bayesglm
invlogit	invlogit
LMERlike-class	LMERlike-class
LMlike-class	LMlike-class
logFC	logFC
logLik,GLMlike-method	LMlike-class
logLik,LMERlike-method	LMERlike-class
logmean	logmean
LRT	LRT
LRT,SingleCellAssay,character-method	LRT
lrTest	lrTest
lrTest,LMlike,character-method	LMlike-class
lrTest,LMlike,CoefficientHypothesis-method	LMlike-class
lrTest,LMlike,Hypothesis-method	LMlike-class
lrTest,LMlike,matrix-method	LMlike-class
lrTest,ZlmFit,character-method	lrTest-ZlmFit-character-method
lrTest,ZlmFit,CoefficientHypothesis-method	ZlmFit-class
lrTest,ZlmFit,Hypothesis-method	ZlmFit-class
lrTest,ZlmFit,matrix-method	ZlmFit-class
magic_assay_names	defaultAssay
maits	maits-dataset
MAST	MAST-package
mast_filter	mast_filter
melt.SingleCellAssay	melt.SingleCellAssay
model.matrix	model.matrix
model.matrix,LMlike-method	model.matrix
model.matrix<-	model.matrix-set
myBiplot	myBiplot
numexp	freq
partialScore	collectResiduals
pbootVcov1	pbootVcov1
plot.thresholdSCRNACountMatrix	plot.thresholdSCRNACountMatrix
plotlrt	plotlrt
plotSCAConcordance	plotSCAConcordance
predict.ZlmFit	predict.ZlmFit
primerAverage	primerAverage
print.summaryThresholdSCRNA	summary.thresholdSCRNACountMatrix
print.summaryZlmFit	print.summaryZlmFit
read.fluidigm	read.fluidigm
removeResponse	removeResponse
rstandard.bayesglm	rstandard.bayesglm
se.coef	se.coef
se.coef,ZlmFit-method	ZlmFit-class
show,LMlike-method	show
show,ZlmFit-method	show
SingleCellAssay	FromFlatDF
split,SingleCellAssay,character-method	split-SingleCellAssay-character-method
split,SingleCellAssay,factor-method	split-SingleCellAssay-character-method
split,SingleCellAssay,list-method	split-SingleCellAssay-character-method
stat_ell	stat_ell
subset,SingleCellAssay-method	subset-SingleCellAssay-method
summarize	summarize
summary,GSEATests-method	summary-GSEATests-method
summary,LMlike-method	LMlike-class
summary,ZlmFit-method	summary-ZlmFit-method
summary.thresholdSCRNACountMatrix	summary.thresholdSCRNACountMatrix
thresholdSCRNACountMatrix	thresholdSCRNACountMatrix
update,LMERlike-method	LMERlike-class
update,LMlike-method	LMlike-class
vbeta	vbeta-dataset
vbetaFA	vbetaFA-dataset
vcov,GLMlike-method	GLMlike-class
vcov,LMERlike-method	LMERlike-class
vcov,ZlmFit-method	ZlmFit-class
waldTest	waldTest
waldTest,LMlike,CoefficientHypothesis-method	LMlike-class
waldTest,LMlike,matrix-method	LMlike-class
waldTest,ZlmFit,CoefficientHypothesis-method	ZlmFit-class
waldTest,ZlmFit,Hypothesis-method	ZlmFit-class
waldTest,ZlmFit,matrix-method	waldTest-ZlmFit-matrix-method
xform	xform
zlm	zlm
zlm.SingleCellAssay	zlm
ZlmFit	ZlmFit-class
ZlmFit-class	ZlmFit-class
