addKpredictions	addKpredictions
adjustFluo	adjustFluo
aveDiff	aveDiff
BatchFluo	BatchFluo
BGcorrectFluo	BGcorrectFluo
boxcoxMatrix	boxcoxMatrix
boxcoxMatrixEst	boxcoxMatrixEst
boxFluo	boxFluo
caseof0s	caseof0s
caseof1R0G	caseof1R0G
caseof1R1G	caseof1R1G
caseof1R2G	caseof1R2G
caseof2R1G	caseof2R1G
caseof2R2G	caseof2R2G
caseof2Rs0G	caseof2Rs0G
clu	clu
cluster2outlier	cluster2outlier
contrastFluo	contrastFluo
cpoints	cpoints
cpPELT	cpPELT
createFluo	createFluo
cutpointsEstimator	cutpointsEstimator
CVsampler	CVsampler
DDHFfit	DDHFfit
DDHFinput	DDHFinput
ddhft.np.2	ddhft.np.2
defineLocClusters	defineLocClusters
denoisefun	denoisefun
denoiser	denoiser
despecklefun	despecklefun
diagnoseResiduals	diagnoseResiduals
distfromcenter	distfromcenter
doTransform	doTransform
estimate.new.pseudotimes	estimate.new.pseudotimes
estimatePath	estimatePath
estimates	estimates
estimates.2	estimates.2
extractBFArea	extractBFArea
failurecase	failurecase
fclust	fclust
files	files
filled.contour3	filled.contour3
findPattern	findPattern
fixPath	fixPath
flowclust_step1	flowclust_step1
flowclust_step2	flowclust_step2
FluoInspection	FluoInspection
FluoSelection_byRun	FluoSelection_byRun
Fluo_adjustment	Fluo_adjustment
Fluo_CV_modeling	Fluo_CV_modeling
Fluo_CV_prep	Fluo_CV_prep
Fluo_inspection	Fluo_inspection
Fluo_modeling	Fluo_modeling
Fluo_ordering	Fluo_ordering
forceBF	forceBF
function.from.vector	function.from.vector
GAPanalysis	GAPanalysis
getCoordinates_stats	getCoordinates_stats
getCsFAIL	getCsFAIL
getFluo	getFluo
getFluo_byRun	getFluo_byRun
getSpot	getSpot
giveWarning	giveWarning
grouplines	grouplines
grubbs	grubbs
GrubbsOutliers	GrubbsOutliers
highlight.cols	highlight.cols
invTransform	invTransform
isotone	isotone
joinAreas	joinAreas
listSorter	listSorter
lmFluo	lmFluo
LocationMatrix	LocationMatrix
mean_signal	mean_signal
measureB	measureB
measureF	measureF
multiplot	multiplot
myt	myt
orderFluo	orderFluo
path.initiator	path.initiator
pathEstimator	pathEstimator
pathUpdater	pathUpdater
plotImages	plotImages
plot_clusgap	plot_clusgap
predict.kmeans	predict.kmeans
processImg	processImg
project	project
readChaImg	readChaImg
readFiles	readFiles
readOriImg	readOriImg
reestimate.pseudos.byCV	reestimate.pseudos.byCV
refineMixes	refineMixes
Results	Results
revDDHFinput	revDDHFinput
signal.from.matrix	signal.from.matrix
significantSignal	significantSignal
simcells	simcells
sortCentroids	sortCentroids
spot.simulator	spot.simulator
SpotbyStrLines	SpotbyStrLines
spotCenter	spotCenter
spotCoords	spotCoords
spotEstimator	spotEstimator
SpotStats	SpotStats
step1	step1
step2	step2
step2.1	step2.1
step3	step3
step3.1	step3.1
step4	step4
steps2_4	steps2_4
straightColLines	straightColLines
straightRowLines	straightRowLines
subsetAnalysis	subsetAnalysis
summarizeAdjFluo	summarizeAdjFluo
transformFluo	transformFluo
trigofun	trigofun
unnormalizeC01	unnormalizeC01
updateCentroids	updateCentroids
updateCentroidsPaths	updateCentroidsPaths
which.min.diff	which.min.diff
zoomInBF	zoomInBF
