CONFESS: Cell OrderiNg by FluorEScence Signal

Single Cell Fluidigm Spot Detector.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CONFESS")
AuthorDiana LOW and Efthimios MOTAKIS
Bioconductor views CellBiology Classification Clustering DataImport GeneExpression QualityControl RNASeq Regression TimeCourse Visualization
Date of publicationNone
MaintainerDiana LOW <dlow@imcb.a-star.edu.sg>
LicenseGPL-2
Version1.4.0

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

Functions

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

Files

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

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