CONFESS: Cell OrderiNg by FluorEScence Signal

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Single Cell Fluidigm Spot Detector.

Author
Diana LOW and Efthimios MOTAKIS
Date of publication
None
Maintainer
Diana LOW <dlow@imcb.a-star.edu.sg>
License
GPL-2
Version
1.2.0

View on Bioconductor

Man pages

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
Fluo_adjustment
Fluo_adjustment
Fluo_CV_modeling
Fluo_CV_modeling
Fluo_CV_prep
Fluo_CV_prep
Fluo_inspection
Fluo_inspection
FluoInspection
FluoInspection
Fluo_modeling
Fluo_modeling
Fluo_ordering
Fluo_ordering
FluoSelection_byRun
FluoSelection_byRun
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
pathEstimator
pathEstimator
path.initiator
path.initiator
pathUpdater
pathUpdater
plot_clusgap
plot_clusgap
plotImages
plotImages
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
SpotbyStrLines
SpotbyStrLines
spotCenter
spotCenter
spotCoords
spotCoords
spotEstimator
spotEstimator
spot.simulator
spot.simulator
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

Files in this package

CONFESS/.BBSoptions
CONFESS/DESCRIPTION
CONFESS/NAMESPACE
CONFESS/NEWS
CONFESS/R
CONFESS/R/cases.R
CONFESS/R/fluo_NBE.R
CONFESS/R/fluo_est.R
CONFESS/R/internal_DDHF.R
CONFESS/R/internal_fluo_NBE.R
CONFESS/R/internal_fluo_est.R
CONFESS/R/simulator.R
CONFESS/build
CONFESS/build/vignette.rds
CONFESS/data
CONFESS/data/Results.rda
CONFESS/data/clu.rda
CONFESS/data/estimates.2.rda
CONFESS/data/estimates.rda
CONFESS/data/files.rda
CONFESS/data/step1.rda
CONFESS/data/step2.1.rda
CONFESS/data/step2.rda
CONFESS/data/step3.1.rda
CONFESS/data/step3.rda
CONFESS/data/step4.rda
CONFESS/data/steps2_4.rda
CONFESS/inst
CONFESS/inst/doc
CONFESS/inst/doc/vignette.R
CONFESS/inst/doc/vignette.Rmd
CONFESS/inst/doc/vignette.html
CONFESS/inst/doc/vignette_tex.R
CONFESS/inst/doc/vignette_tex.Rnw
CONFESS/inst/doc/vignette_tex.pdf
CONFESS/inst/extdata
CONFESS/inst/extdata/Results_of_image_analysis.txt
CONFESS/man
CONFESS/man/BGcorrectFluo.Rd
CONFESS/man/BatchFluo.Rd
CONFESS/man/CVsampler.Rd
CONFESS/man/DDHFfit.Rd
CONFESS/man/DDHFinput.Rd
CONFESS/man/FluoInspection.Rd
CONFESS/man/FluoSelection_byRun.Rd
CONFESS/man/Fluo_CV_modeling.Rd
CONFESS/man/Fluo_CV_prep.Rd
CONFESS/man/Fluo_adjustment.Rd
CONFESS/man/Fluo_inspection.Rd
CONFESS/man/Fluo_modeling.Rd
CONFESS/man/Fluo_ordering.Rd
CONFESS/man/GAPanalysis.Rd
CONFESS/man/GrubbsOutliers.Rd
CONFESS/man/LocationMatrix.Rd
CONFESS/man/Results.Rd
CONFESS/man/SpotStats.Rd
CONFESS/man/SpotbyStrLines.Rd
CONFESS/man/addKpredictions.Rd
CONFESS/man/adjustFluo.Rd
CONFESS/man/aveDiff.Rd
CONFESS/man/boxFluo.Rd
CONFESS/man/boxcoxMatrix.Rd
CONFESS/man/boxcoxMatrixEst.Rd
CONFESS/man/caseof0s.Rd
CONFESS/man/caseof1R0G.Rd
CONFESS/man/caseof1R1G.Rd
CONFESS/man/caseof1R2G.Rd
CONFESS/man/caseof2R1G.Rd
CONFESS/man/caseof2R2G.Rd
CONFESS/man/caseof2Rs0G.Rd
CONFESS/man/clu.Rd
CONFESS/man/cluster2outlier.Rd
CONFESS/man/contrastFluo.Rd
CONFESS/man/cpPELT.Rd
CONFESS/man/cpoints.Rd
CONFESS/man/createFluo.Rd
CONFESS/man/cutpointsEstimator.Rd
CONFESS/man/ddhft.np.2.Rd
CONFESS/man/defineLocClusters.Rd
CONFESS/man/denoisefun.Rd
CONFESS/man/denoiser.Rd
CONFESS/man/despecklefun.Rd
CONFESS/man/diagnoseResiduals.Rd
CONFESS/man/distfromcenter.Rd
CONFESS/man/doTransform.Rd
CONFESS/man/estimate.new.pseudotimes.Rd
CONFESS/man/estimatePath.Rd
CONFESS/man/estimates.2.Rd
CONFESS/man/estimates.Rd
CONFESS/man/extractBFArea.Rd
CONFESS/man/failurecase.Rd
CONFESS/man/fclust.Rd
CONFESS/man/files.Rd
CONFESS/man/filled.contour3.Rd
CONFESS/man/findPattern.Rd
CONFESS/man/fixPath.Rd
CONFESS/man/flowclust_step1.Rd
CONFESS/man/flowclust_step2.Rd
CONFESS/man/forceBF.Rd
CONFESS/man/function.from.vector.Rd
CONFESS/man/getCoordinates_stats.Rd
CONFESS/man/getCsFAIL.Rd
CONFESS/man/getFluo.Rd
CONFESS/man/getFluo_byRun.Rd
CONFESS/man/getSpot.Rd
CONFESS/man/giveWarning.Rd
CONFESS/man/grouplines.Rd
CONFESS/man/grubbs.Rd
CONFESS/man/highlight.cols.Rd
CONFESS/man/invTransform.Rd
CONFESS/man/isotone.Rd
CONFESS/man/joinAreas.Rd
CONFESS/man/listSorter.Rd
CONFESS/man/lmFluo.Rd
CONFESS/man/mean_signal.Rd
CONFESS/man/measureB.Rd
CONFESS/man/measureF.Rd
CONFESS/man/multiplot.Rd
CONFESS/man/myt.Rd
CONFESS/man/orderFluo.Rd
CONFESS/man/path.initiator.Rd
CONFESS/man/pathEstimator.Rd
CONFESS/man/pathUpdater.Rd
CONFESS/man/plotImages.Rd
CONFESS/man/plot_clusgap.Rd
CONFESS/man/predict.kmeans.Rd
CONFESS/man/processImg.Rd
CONFESS/man/project.Rd
CONFESS/man/readChaImg.Rd
CONFESS/man/readFiles.Rd
CONFESS/man/readOriImg.Rd
CONFESS/man/reestimate.pseudos.byCV.Rd
CONFESS/man/refineMixes.Rd
CONFESS/man/revDDHFinput.Rd
CONFESS/man/signal.from.matrix.Rd
CONFESS/man/significantSignal.Rd
CONFESS/man/simcells.Rd
CONFESS/man/sortCentroids.Rd
CONFESS/man/spot.simulator.Rd
CONFESS/man/spotCenter.Rd
CONFESS/man/spotCoords.Rd
CONFESS/man/spotEstimator.Rd
CONFESS/man/step1.Rd
CONFESS/man/step2.1.Rd
CONFESS/man/step2.Rd
CONFESS/man/step3.1.Rd
CONFESS/man/step3.Rd
CONFESS/man/step4.Rd
CONFESS/man/steps2_4.Rd
CONFESS/man/straightColLines.Rd
CONFESS/man/straightRowLines.Rd
CONFESS/man/subsetAnalysis.Rd
CONFESS/man/summarizeAdjFluo.Rd
CONFESS/man/transformFluo.Rd
CONFESS/man/trigofun.Rd
CONFESS/man/unnormalizeC01.Rd
CONFESS/man/updateCentroids.Rd
CONFESS/man/updateCentroidsPaths.Rd
CONFESS/man/which.min.diff.Rd
CONFESS/man/zoomInBF.Rd
CONFESS/vignettes
CONFESS/vignettes/defineLocClusters.jpeg
CONFESS/vignettes/fluo_CV_modeling.jpeg
CONFESS/vignettes/fluo_CV_modeling_2.jpeg
CONFESS/vignettes/fluo_adjustment.jpeg
CONFESS/vignettes/fluo_inspection_GAP.jpeg
CONFESS/vignettes/fluo_inspection_clusters.jpeg
CONFESS/vignettes/fluo_ordering.jpeg
CONFESS/vignettes/spotEstimator.jpeg
CONFESS/vignettes/spotEstimator2.jpeg
CONFESS/vignettes/vignette.Rmd
CONFESS/vignettes/vignette_tex.Rnw