MAST-package	MAST-package
"summary-ZlmFit",	summary-ZlmFit-method
"ZlmFit-summary"	summary-ZlmFit-method
applyFlat	applyFlat
assay,SingleCellAssay,missing-method	defaultAssay
assay_idx	defaultAssay
BayesGLMlike-class	BayesGLMlike-class
bootVcov1	bootVcov1
burdenOfFiltering	mast_filter
calcZ	calcZ
cData	MAST-defunct
coef,LMERlike-method	LMERlike-class
coef,ZlmFit-method	ZlmFit-class
CoefficientHypothesis	Hypothesis
colData<-,SingleCellAssay,DataFrame-method	colData-set-SingleCellAssay-DataFrame-method
collectResiduals	collectResiduals
combined_residuals_hook	collectResiduals
computeEtFromCt	computeEtFromCt
condmean	freq
condSd	freq
continuous_residuals_hook	collectResiduals
convertMASTClassicToSingleCellAssay	convertMASTClassicToSingleCellAssay
CovFromBoots	CovFromBoots
defaultAssay	defaultAssay
defaultPrior	defaultPrior
deviance_residuals_hook	collectResiduals
discrete_residuals_hook	collectResiduals
dof	dof
dof,GLMlike-method	dof
dof,LMERlike-method	dof
Drop	Drop
ebayes	ebayes
expavg	expavg
exprs	MAST-defunct
fData	MAST-defunct
filter	MAST-defunct
filterLowExpressedGenes	filterLowExpressedGenes
fit	fit
fit,BayesGLMlike,missing-method	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
gsea_control	gseaAfterBoot
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-defunct	MAST-defunct
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
predicted_sig	predicted_sig-dataset
primerAverage	primerAverage
print.summaryThresholdSCRNA	summary.thresholdSCRNACountMatrix
print.summaryZlmFit	print.summaryZlmFit
read.fluidigm	read.fluidigm
removeResponse	removeResponse
rstandard.bayesglm	rstandard.bayesglm
SceToSingleCellAssay	SceToSingleCellAssay
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
