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CONFESS (version 1.0.2)

Cell OrderiNg by FluorEScence Signal

Description

Single Cell Fluidigm Spot Detector.

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Version

Version

1.0.2

License

GPL-2

Maintainer

Diana LOW

Last Published

February 15th, 2017

Functions in CONFESS (1.0.2)

joinAreas

joinAreas
FluoInspection

FluoInspection
adjustFluo

adjustFluo
caseof2R2G

caseof2R2G
defineLocClusters

defineLocClusters
getCoordinates_stats

getCoordinates_stats
orderFluo

orderFluo
denoiser

denoiser
step3

step3
caseof2Rs0G

caseof2Rs0G
caseof1R0G

caseof1R0G
estimates

estimates
fixPath

FixPath
failurecase

failurecase
project

project
signal.from.matrix

signal.from.matrix
which.min.diff

which.min.diff
Fluo_modeling

Fluo_modeling
BatchFluo

BatchFluo
BGcorrectFluo

BGcorrectFluo
Fluo_ordering

Fluo_ordering
FluoSelection_byRun

FluoSelection_byRun
addKpredictions

addKpredictions
aveDiff

aveDiff
SpotbyStrLines

SpotbyStrLines
caseof2R1G

caseof2R1G
boxFluo

boxFluo
SpotStats

spotStats
GAPanalysis

GAPanalysis
caseof1R2G

caseof1R2G
estimates.2

estimates.2
mean_signal

mean_signal
getSpot

getSpot
createFluo

createFluo
readOriImg

readOriImg
contrastFluo

contrastFluo
despecklefun

despecklefun
denoisefun

denoisefun
distfromcenter

distfromcenter
revDDHFinput

revDDHFinput
updateCentroidsPaths

updateCentroidsPaths
reestimate.pseudos.byCV

reestimate.pseudos.byCV
extractBFArea

extractBFarea
cluster2outlier

cluster2outlier
plot_clusgap

plot_clusgap
highlight.cols

highlight.cols
sortCentroids

sortCentroids
caseof1R1G

caseof1R1G
straightRowLines

straightRowLines
myt

myt
predict.kmeans

predict.kmeans
flowclust_step1

flowclust_step1
doTransform

doTransform
cpPELT

cpPELT
filled.contour3

filled.contour3
grouplines

grouplines
LocationMatrix

LocationMatrix
giveWarning

giveWarning
readFiles

readFiles
processImg

processImg
plotImages

plotImages
subsetAnalysis

subsetAnalysis
significantSignal

significantSignal
step1

step1
spotEstimator

spotEstimator
refineMixes

refineMixes
summarizeAdjFluo

summarizeAdjFluo
spot.simulator

spot.simulator
GrubbsOutliers

GrubbsOutliers
Fluo_adjustment

Fluo_adjustment
Fluo_inspection

Fluo_inspection
findPattern

findPattern
fclust

fclust
getCsFAIL

getCsFAIL
forceBF

forceBF
listSorter

listSorter
Fluo_CV_prep

Fluo_CV_prep
spotCoords

spotCoords
DDHFinput

DDHFinput
step2

step2
trigofun

trigofun
straightColLines

straightColLines
cpoints

cpoints
cutpointsEstimator

cutpointsEstimator
estimatePath

estimatePath
getFluo_byRun

getFluo_byRun
invTransform

invTransform
simcells

simcells
spotCenter

spotCenter
zoomInBF

zoomInBF
caseof0s

caseof0s
Fluo_CV_modeling

Fluo_CV_modeling
estimate.new.pseudotimes

estimate.new.pseudotimes
flowclust_step2

flowclust_step2
files

files
grubbs

grubbs
isotone

isotone
measureB

measureB
pathEstimator

pathEstimator
diagnoseResiduals

diagnoseResiduals
path.initiator

path.initiator
updateCentroids

updateCentroids
transformFluo

transformFluo
CVsampler

CVsampler
DDHFfit

DDHFfit
getFluo

getFluo
lmFluo

lmFluo
pathUpdater

pathUpdater
step4

step4
step3.1

step3.1
boxcoxMatrixEst

boxcoxMatrixEst
Results

Results
clu

clu
boxcoxMatrix

boxcoxMatrix
function.from.vector

function.from.vector
ddhft.np.2

ddhft.np.2
multiplot

multiplot
measureF

measureF
step2.1

step2.1
readChaImg

readChaImg
steps2_4

steps2_4
unnormalizeC01

unnormalizeC01