flowCore: flowCore: Basic structures for flow cytometry data

Provides S4 data structures and basic functions to deal with flow cytometry data.

AuthorB. Ellis, P. Haaland, F. Hahne, N. Le Meur, N. Gopalakrishnan, J. Spidlen, M. Jiang
Date of publicationNone
MaintainerM.Jiang <wjiang2@fhcrc.org>
LicenseArtistic-2.0
Version1.40.4

View on Bioconductor

Man pages

actionItem-class: Class "actionItem"

arcsinhTransform: Create the definition of an arcsinh transformation function...

asinht-class: Class "asinht"

asinhtGml2-class: Class asinhtGml2

biexponentialTransform: Compute a transform using the 'biexponential' function

boundaryFilter-class: Class "boundaryFilter"

characterOrTransformation-class: Class "characterOrTransformation"

checkOffset: Fix the offset when its values recorded in header and TEXT...

coerce: Convert an object to another class

compensateActionItem-class: Class "compensateActionItem"

compensatedParameter-class: Class "compensatedParameter"

compensateView-class: Class "compensateView"

compensation-class: Class "compensation"

concreteFilter-class: Class "concreteFilter"

dg1polynomial-class: Class "dg1polynomial"

each_col-methods: Method to apply functions over flowFrame margins

EHtrans-class: Class "EHtrans"

ellipsoidGate: Class "ellipsoidGate"

estimateMedianLogicle: Estimates a common logicle transformation for a flowSet.

exponential-class: Class "exponential"

expressionFilter-class: Class "expressionFilter"

fcReference-class: Class "fcReference" and its subclasses

FCSTransTransform: Computes a transform using the 'iplogicle' function

filter-and-methods: Take the intersection of two filters

filter-class: A class for representing filtering operations to be applied...

filterDetails-methods: Obtain details about a filter operation

filter-in-methods: Filter-specific membership methods

filterList-class: Class "filterList"

filter-methods: Filter FCS files

filter-on-methods: Methods for Function %on% in Package 'flowCore'

filterReference-class: Class filterReference

filterResult-class: Class "filterResult"

filterResultList-class: Class "filterResultList"

filters-class: Class "filters" and "filtersList"

filterSet-class: Class filterSet(deprecated)

filterSummary-class: Class "filterSummary"

filterSummaryList-class: Class "filterSummaryList"

flowCore-package: Provides S4 data structures and basic infrastructure and...

flowFrame-class: 'flowFrame': a class for storing observed quantitative...

flowSet-class: 'flowSet': a class for storing flow cytometry raw data from...

fsApply: Apply a Function over values in a flowSet

gateActionItem-class: Class "gateActionItem"

gateView-class: Class "gateView"

getChannelMarker: get channel and marker information from a 'flowFrame' that...

getIndexSort-methods: Extract Index Sorted Data from an FCS File

GvHD: Extract of a Graft versus Host Disease monitoring experiment...

hyperlog-class: Class "hyperlog"

hyperlogtGml2-class: Class hyperlogtGml2

identifier-methods: Retrieve the GUID of flowCore objects

inverseLogicleTransform: Computes the inverse of the transform defined by the...

invsplitscale-class: Class "invsplitscale"

keyword-methods: Methods to retrieve keywords of a flowFrame

kmeansFilter: Class "kmeansFilter"

linearTransform: Create the definition of a linear transformation function to...

lintGml2-class: Class lintGml2

lnTransform: Create the definition of a ln transformation function...

logarithm-class: Class "logarithm"

logicalFilterResult-class: Class "logicalFilterResult"

logicletGml2-class: Class logicletGml2

logicleTransform: Computes a transform using the 'logicle_transform' function

logtGml2-class: Class logtGml2

logTransform: Create the definition of a log transformation function (base...

manyFilterResult-class: Class "manyFilterResult"

markernames: get or update the marker names

multipleFilterResult-class: Class "multipleFilterResult"

norm2Filter-class: Class "norm2Filter"

normalization-class: Class "normalization"

normalizeActionItem-class: Class "normalizeActionItem"

normalizeView-class: Class "normalizeView"

parameterFilter-class: Class "parameterFilter"

parameters-class: Class "parameters"

parameters-methods: Obtain information about parameters for flow cytometry...

parameterTransform-class: Class "parameterTransform"

polygonGate: Class "polygonGate"

polytopeGate: Define filter boundaries

quadGate: Class "quadGate"

quadratic-class: Class "quadratic"

quadraticTransform: Create the definition of a quadratic transformation function...

randomFilterResult-class: Class "randomFilterResult"

ratio-class: Class "ratio"

ratiotGml2-class: Class "ratiotGml2"

read.FCS: Read an FCS file

read.FCSheader: Read the TEXT section of a FCS file

read.flowSet: Read a set of FCS files

rectangleGate: Class "rectangleGate"

sampleFilter-class: Class "sampleFilter"

scaleTransform: Create the definition of a scale transformation function to...

setOperationFilter-class: Class "setOperationFilter"

singleParameterTransform-class: Class "singleParameterTransform"

sinht-class: Class "sinht"

spillover-flowSet: Compute a spillover matrix from a flowSet

split-methods: Methods to split flowFrames and flowSets according to filters

splitscale-class: Class "splitscale"

splitScaleTransform: Compute the split-scale transformation describe by FL. Battye

squareroot-class: Class "squareroot"

Subset-methods: Subset a flowFrame or a flowSet

subsettingActionItem-class: Class "subsettingActionItem"

subsetting-class: Class "subsetting"

subsettingView-class: Class "subsettingView"

summarizeFilter-methods: Methods for function summarizeFilter

timeFilter-class: Class "timeFilter"

transformActionItem-class: Class "transformActionItem"

transformation-class: Class "transformation"

transform-class: 'transform': a class for transforming flow-cytometry data by...

transformFilter-class: A class for encapsulating a filter to be performed on...

transformList-class: Class "transformList"

transformMap-class: A class for mapping transforms between parameters

transformReference-class: Class "transformReference"

transformView-class: Class "transformView"

truncateTransform: Create the definition of a truncate transformation function...

unitytransform-class: Class "unitytransform"

validFilters: Check if all filters in a filters matches same paramters

view-class: Class "view"

workFlow-class: Class "workFlow"(deprecated)

write.FCS: Write an FCS file

write.flowSet: Write an FCS file

Functions

\%&\% Man page
action Man page
actionItem-class Man page
actions Man page
actions,workFlow-method Man page
action,view-method Man page
add Man page
add,workFlow,character-method Man page
add,workFlow,compensation-method Man page
add,workFlow,concreteFilter-method Man page
add,workFlow,filterList-method Man page
add,workFlow,logical-method Man page
add,workFlow,normalization-method Man page
add,workFlow,numeric-method Man page
add,workFlow,subsetting-method Man page
add,workFlow,transformList-method Man page
alias Man page
alias,actionItem-method Man page
alias,environment-method Man page
alias,view-method Man page
alias,workFlow-method Man page
\%&\%,ANY-method Man page
arcsinhTransform Man page
as.data.frame.manyFilterResult Man page
asinht Man page
asinht-class Man page
asinhtGml2 Man page
asinhtGml2-class Man page
assign Man page
assign,ANY,ANY,missing,workFlow,missing,missing-method Man page
assign,character,ANY,workFlow,missing,missing,missing-method Man page
assign,fcReference,ANY,workFlow,missing,missing,missing-method Man page
assign,missing,ANY,missing,workFlow,missing,missing-method Man page
assign,missing,ANY,workFlow,missing,missing,missing-method Man page
biexponentialTransform Man page
booleanGate,filter-class Man page
boundaryFilter Man page
boundaryFilter-class Man page
call,filter-method Man page
cbind2,flowFrame,matrix-method Man page
cbind2,flowFrame,numeric-method Man page
char2ExpressionFilter Man page
character,filter-method Man page
characterOrTransformation-class Man page
checkOffset Man page
cleanup Man page
coerce Man page
coerce,call,filter-method Man page
coerce,character,filter-method Man page
coerce,complementFilter,call-method Man page
coerce,complementFilter,logical-method Man page
coerce,ellipsoidGate,polygonGate-method Man page
coerce,environment,flowSet-method Man page
coerce,factor,filterResult-method Man page
coerce,filter,call-method Man page
coerce,filter,logical-method Man page
coerce,filterReference,call-method Man page
coerce,filterReference,concreteFilter-method Man page
coerce,filterResultList,list-method Man page
coerce,filterResult,logical-method Man page
coerce,filterSet,list-method Man page
coerce,filterSummary,data.frame-method Man page
coerce,flowFrame,filterSet-method Man page
coerce,flowFrame,flowSet-method Man page
coerce,flowSet,flowFrame-method Man page
coerce,flowSet,list-method Man page
coerce,formula,filter-method Man page
coerce,gateView,filterResult-method Man page
coerce,intersectFiler,call-method Man page
coerce,intersectFilter,call-method Man page
coerce,intersectFilter,logical-method Man page
coerce,list,filterResultList-method Man page
coerce,list,filterSet-method Man page
coerce,list,flowSet-method Man page
coerce,list,transformList-method Man page
coerce,logicalFilterResult,logical-method Man page
coerce,logical,filterResult-method Man page
coerce,matrix,filterResult-method Man page
coerce,name,filter-method Man page
coerce,nullParameter,character-method Man page
coerce,numeric,filterResult-method Man page
coerce,parameters,character-method Man page
coerce,randomFilterResult,logical-method Man page
coerce,ratio,character-method Man page
coerce,rectangleGate,polygonGate-method Man page
coerce,subsetFilter,call-method Man page
coerce,subsetFilter,logical-method Man page
coerce,transform,character-method Man page
coerce,unionFilter,call-method Man page
coerce,unionFilter,logical-method Man page
coerce,unitytransform,character-method Man page
colnames<- Man page
colnames<-,flowFrame-method Man page
colnames,flowFrame-method Man page
colnames<-,flowSet-method Man page
colnames,flowSet-method Man page
colnames,transformList-method Man page
compensate Man page
compensateActionItem Man page
compensateActionItem-class Man page
compensatedParameter Man page
compensatedParameter-class Man page
compensate,flowFrame,compensation-method Man page
compensate,flowFrame,data.frame-method Man page
compensate,flowFrame,matrix-method Man page
compensate,flowSet,ANY-method Man page
compensate,flowSet,data.frame-method Man page
compensate,flowSet,list-method Man page
compensateView Man page
compensateView-class Man page
compensation Man page
compensation-class Man page
complementFilter-class Man page
concreteFilter-class Man page
c,transformList-method Man page
Data Man page
Data,view-method Man page
decisionTreeGate,filter-class Man page
description Man page
description<-,flowFrame,ANY-method Man page
description<-,flowFrame,list-method Man page
description,flowFrame-method Man page
dg1polynomial Man page
dg1polynomial-class Man page
dim Man page
dim,flowFrame-method Man page
each_col Man page
each_col,flowFrame-method Man page
each_col-methods Man page
each_row Man page
each_row,flowFrame-method Man page
each_row-methods Man page
EHtrans Man page
EHtrans-class Man page
ellipsoidGate Man page
ellipsoidGate-class Man page
ellipsoidGate,filter-class Man page
estimateLogicle Man page
estimateMedianLogicle Man page
eval,asinhtGml2,missing-method Man page
eval,asinht,missing-method Man page
eval,compensatedParameter,missing-method Man page
eval,dg1polynomial,missing-method Man page
eval,EHtrans,missing-method Man page
eval,exponential,missing-method Man page
eval,filterReference,missing-method Man page
eval,hyperlog,missing-method Man page
eval,hyperlogtGml2,missing-method Man page
eval,invsplitscale,missing-method Man page
eval,lintGml2,missing-method Man page
eval,logarithm,missing-method Man page
eval,logicletGml2,missing-method Man page
eval,logtGml2,missing-method Man page
eval,quadratic,missing-method Man page
eval,ratio,missing-method Man page
eval,ratiotGml2,missing-method Man page
eval,sinht,missing-method Man page
eval,splitscale,missing-method Man page
eval,squareroot,missing-method Man page
eval,transformReference,missing-method Man page
eval,unitytransform,missing-method Man page
exponential Man page
exponential-class Man page
expressionFilter Man page
expressionFilter-class Man page
exprs Man page
exprs<- Man page
exprs<-,flowFrame,ANY-method Man page
exprs<-,flowFrame,matrix-method Man page
exprs,flowFrame-method Man page
fcActionReference Man page
fcActionReference-class Man page
fcAliasReference Man page
fcAliasReference-class Man page
fcCompensateReference Man page
fcCompensateReference-class Man page
fcDataReference Man page
fcDataReference-class Man page
fcFilterReference Man page
fcFilterReference-class Man page
fcFilterResultReference Man page
fcFilterResultReference-class Man page
fcNormalizationReference Man page
fcNormalizationReference-class Man page
fcNullReference Man page
fcNullReference-class Man page
fcReference Man page
fcReference-class Man page
FCSTransTransform Man page
fcStructureReference-class Man page
fcSubsettingReference Man page
fcSubsettingReference-class Man page
fcTransformReference Man page
fcTransformReference-class Man page
fcTreeReference Man page
fcTreeReference-class Man page
fcViewReference Man page
fcViewReference-class Man page
featureNames Man page
featureNames,flowFrame-method Man page
filter Man page
filter-class Man page
filterDetails Man page
filterDetails<- Man page
filterDetails,filterResult,ANY-method Man page
filterDetails<-,filterResult,character,ANY-method Man page
filterDetails<-,filterResult,character,filter-method Man page
filterDetails<-,filterResult,character,setOperationFilter-method Man page
filterDetails,filterResult,missing-method Man page
filterDetails-methods Man page
|,filter,filter-method Man page
\%&\%,filter,filter-method Man page
&,filter,filter-method Man page
filter,filter-method Man page
filter,flowFrame,filter-method Man page
filter,flowFrame,filterSet-method Man page
filter,flowFrame-method Man page
filter,flowFrame,norm2Filter Man page
filter,flowFrame,polygonGate Man page
filter,flowFrame,rectangleGate Man page
filter,flowSet,filterList-method Man page
filter,flowSet,filter-method Man page
filter,flowSet,filterSet-method Man page
filter,flowSet,list-method Man page
filtergate,filter-class Man page
filterList Man page
filterList-class Man page
|,filter,list-method Man page
&,filter,list-method Man page
!,filter-method Man page
filter-on-methods Man page
filterReference Man page
filterReference-class Man page
filterReference,environment,character-method Man page
filterReference,filterSet,character-method Man page
filterResult Man page
[[,filterResult,ANY-method Man page
filterResult-class Man page
==,filterResult,flowFrame-method Man page
filterResultList Man page
[,filterResultList,ANY-method Man page
[[,filterResultList,ANY-method Man page
filterResultList-class Man page
filters Man page
filters-class Man page
filterSet Man page
[[<-,filterSet,ANY,ANY,filterReference-method Man page
[[<-,filterSet,character,ANY,filter-method Man page
[[<-,filterSet,character,ANY,formula-method Man page
[,filterSet,character-method Man page
[[,filterSet,character-method Man page
filterSet-class Man page
[[<-,filterSet,missing,ANY,filter Man page
[[<-,filterSet,missing,ANY,filter-method Man page
[[<-,filterSet,NULL,ANY,filter-method Man page
[[<-,filterSet,NULL,ANY,formula-method Man page
filtersList Man page
filtersList-class Man page
filterSummary Man page
[[,filterSummary,character-method Man page
filterSummary-class Man page
filterSummaryList Man page
filterSummaryList-class Man page
$,filterSummary-method Man page
[[,filterSummary,numeric-method Man page
flowCore Man page
flowCore-package Man page
flowFrame Man page
$.flowFrame Man page
<=,flowFrame,ANY-method Man page
<,flowFrame,ANY-method Man page
>=,flowFrame,ANY-method Man page
>,flowFrame,ANY-method Man page
[,flowFrame,ANY-method Man page
flowFrame-class Man page
[,flowFrame,filter-method Man page
==,flowFrame,filterResult-method Man page
[,flowFrame,filterResult-method Man page
==,flowFrame,flowFrame-method Man page
[[<-,flowFrame-method Man page
flowSet Man page
[[<-,flowSet,ANY,ANY,flowFrame-method Man page
[,flowSet,ANY-method Man page
[[,flowSet,ANY-method Man page
flowSet-class Man page
[,flowSet-method Man page
[[<-,flowSet-method Man page
[[,flowSet-method Man page
$,flowSet-method Man page
formula,filter-method Man page
fsApply Man page
fsApply,flowSet,ANY Man page
fsApply,flowSet-method Man page
gate Man page
gateActionItem Man page
gateActionItem-class Man page
gate,gateActionItem-method Man page
gateView Man page
gateView-class Man page
getChannelMarker Man page
get,character,missing,workFlow-method Man page
get,character,workFlow,missing-method Man page
get,fcNullReference,missing,missing-method Man page
get,fcReference,missing,missing-method Man page
getIndexSort Man page
getIndexSort,flowFrame-method Man page
GvHD Man page
head,flowFrame-method Man page
hyperlog Man page
hyperlog-class Man page
hyperlogtGml2 Man page
hyperlogtGml2-class Man page
identifier Man page
identifier<- Man page
identifier,actionItem-method Man page
identifier<-,compensation,character-method Man page
identifier,compensation-method Man page
identifier,fcReference-method Man page
identifier<-,filter,character-method Man page
identifier<-,filterList,character-method Man page
identifier,filterList-method Man page
identifier,filter-method Man page
identifier,filterReference-method Man page
identifier,filterResult-method Man page
identifier,filterSet,character-method Man page
identifier,filterSet-method Man page
identifier<-,flowFrame,ANY-method Man page
identifier<-,flowFrame-method Man page
identifier,flowFrame-method Man page
identifier<-,flowSet,ANY-method Man page
identifier,flowSet-method Man page
identifier-methods Man page
identifier<-,normalization,character-method Man page
identifier,normalization-method Man page
identifier,NULL-method Man page
identifier<-,subsetting,character-method Man page
identifier,subsetting-method Man page
identifier<-,transformList,character-method Man page
identifier,transformList-method Man page
identifier,transform-method Man page
identifier,view-method Man page
\%in\% Man page
\%in\%,ANY,filterReference-method Man page
\%in\%,ANY,filterResult-method Man page
\%in\%,ANY,manyFilterResult-method Man page
\%in\%,ANY,multipleFilterResult-method Man page
\%in\%,flowFrame,boundaryFilter-method Man page
\%in\%,flowFrame,complementFilter-method Man page
\%in\%,flowFrame,ellipsoidGate-method Man page
\%in\%,flowFrame,expressionFilter-method Man page
\%in\%,flowFrame,filterResult-method Man page
\%in\%,flowFrame,intersectFilter-method Man page
\%in\%,flowFrame,kmeansFilter-method Man page
\%in\%,flowFrame,norm2Filter-method Man page
\%in\%,flowFrame,polygonGate-method Man page
\%in\%,flowFrame,polytopeGate-method Man page
\%in\%,flowFrame,quadGate-method Man page
\%in\%,flowFrame,rectangleGate-method Man page
\%in\%,flowFrame,sampleFilter-method Man page
\%in\%,flowFrame,subsetFilter-method Man page
\%in\%,flowFrame,timeFilter-method Man page
\%in\%,flowFrame,transformFilter-method Man page
\%in\%,flowFrame,unionFilter-method Man page
initialize,dg1polynomial-method Man page
initialize,flowFrame-method Man page
initialize,parameterFilter-method Man page
initialize,ratio-method Man page
initialize,ratiotGml2-method Man page
initialize,singleParameterTransform-method Man page
\%in\%-methods Man page
intersectFilter-class Man page
intersectFilter-method Man page
inverseLogicleTransform Man page
invsplitscale Man page
invsplitscale-class Man page
isFCSfile Man page
isNull Man page
isNull,fcReference-method Man page
journal Man page
journal,environment-method Man page
journal,workFlow-method Man page
keyword Man page
keyword<- Man page
keyword<-,flowFrame,ANY-method Man page
keyword<-,flowFrame,character-method Man page
keyword,flowFrame,character-method Man page
keyword,flowFrame,function-method Man page
keyword<-,flowFrame,list-method Man page
keyword,flowFrame,list-method Man page
keyword,flowFrame,missing-method Man page
keyword,flowSet,ANY-method Man page
keyword<-,flowSet,list-method Man page
keyword,flowSet,list-method Man page
keyword-methods Man page
kmeansFilter Man page
kmeansFilter-class Man page
length,filter-method Man page
length,filterReference-method Man page
length,filterSummary-method Man page
length,flowSet-method Man page
length,kmeansFilter-method Man page
length,logicalFilterResult-method Man page
length,manyFilterResult-method Man page
length,multipleFilterResult-method Man page
linearTransform Man page
lintGml2 Man page
lintGml2-class Man page
|,list,filter-method Man page
&,list,filter-method Man page
lnTransform Man page
logarithm Man page
logarithm-class Man page
logicalFilterResult Man page
[[,logicalFilterResult,ANY-method Man page
logicalFilterResult-class Man page
logicletGml2 Man page
logicletGml2-class Man page
logicleTransform Man page
logtGml2 Man page
logtGml2-class Man page
logTransform Man page
ls Man page
ls,workFlow,missing,missing,missing,character-method Man page
ls,workFlow,missing,missing,missing,missing-method Man page
manyFilterResult Man page
[[,manyFilterResult,ANY-method Man page
manyFilterResult-class Man page
[[,manyFilterResult-method Man page
markernames Man page
markernames<- Man page
markernames<-,flowFrame-method Man page
markernames,flowFrame-method Man page
markernames<-,flowSet-method Man page
markernames,flowSet-method Man page
\%&\%-methods Man page
mget,character,workFlow-method Man page
multipleFilterResult Man page
[,multipleFilterResult,ANY-method Man page
[[,multipleFilterResult,ANY-method Man page
multipleFilterResult-class Man page
[[,multipleFilterResult-method Man page
name,filter-method Man page
names Man page
names,actionItem-method Man page
names,filterResultList-method Man page
names,filterSet-method Man page
names,filterSummary-method Man page
names,flowFrame-method Man page
names,logicalFilterResult-method Man page
names,manyFilterResult-method Man page
names<-,multipleFilterResult,ANY-method Man page
names<-,multipleFilterResult-method Man page
names,multipleFilterResult-method Man page
names,view-method Man page
names,workFlow-method Man page
ncol,flowFrame-method Man page
nodes,workFlow-method Man page
norm2Filter Man page
norm2Filter-class Man page
norm2Filter,filter-class Man page
normalization Man page
normalization-class Man page
normalize Man page
normalizeActionItem Man page
normalizeActionItem-class Man page
normalize,flowSet,normalization-method Man page
normalizeView Man page
normalizeView-class Man page
nrow,flowFrame-method Man page
\%on\% Man page
\%on\%,ANY,flowSet-method Man page
\%on\%,filter,parameterTransform-method Man page
\%on\%,filter,transformList-method Man page
\%on\%,filter,transform-method Man page
\%on\%-methods Man page
\%on\%,parameterTransform,flowFrame-method Man page
\%on\%,transform,flowFrame-method Man page
\%on\%,transformList,flowFrame-method Man page
\%on\%,transformList,flowSet-method Man page
parameterFilter-class Man page
parameters Man page
parameters<- Man page
parameters-class Man page
parameters,compensation-method Man page
parameters<-,dg1polynomial,character-method Man page
parameters<-,dg1polynomial,parameters-method Man page
parameters<-,dg1polynomial,transform-method Man page
parameters,filter-method Man page
parameters,filterReference-method Man page
parameters,filterResultList-method Man page
parameters,filterResult-method Man page
parameters<-,flowFrame,AnnotatedDataFrame-method Man page
parameters,flowFrame-method Man page
parameters,flowFrame,missing-method Man page
parameters,manyFilterResult-method Man page
parameters,normalization-method Man page
parameters,nullParameter-method Man page
parameters<-,parameterFilter,character-method Man page
parameters<-,parameterFilter,list-method Man page
parameters,parameterFilter-method Man page
parameters<-,parameterFilter,transform-method Man page
parameters,parameterTransform-method Man page
parameters,ratio-method Man page
parameters,ratiotGml2-method Man page
parameters,setOperationFilter-method Man page
parameters<-,singleParameterTransform,character-method Man page
parameters,singleParameterTransform-method Man page
parameters<-,singleParameterTransform,transform-method Man page
parameters,transform-method Man page
parameters,transformReference-method Man page
parameterTransform-class Man page
parent Man page
parent,actionItem-method Man page
parent,NULL-method Man page
parent,view-method Man page
pData<-,flowSet,data.frame-method Man page
pData,flowSet-method Man page
phenoData<-,flowSet,ANY-method Man page
phenoData,flowSet-method Man page
phenoData<-,flowSet,phenoData-method Man page
plot,flowFrame,ANY-method Man page
plot,flowFrame-method Man page
plot,flowSet,ANY-method Man page
plot,flowSet-method Man page
plot,workFlow,missing-method Man page
polygonGate Man page
polygonGate-class Man page
polygonGate,filter-class Man page
polytopeGate Man page
polytopeGate-class Man page
print,compensateActionItem-method Man page
print,filterSummary-method Man page
print,gateActionItem-method Man page
print,normalizeActionItem-method Man page
print,subsettingActionItem-method Man page
print,transformActionItem-method Man page
print,view-method Man page
quadGate Man page
quadGate-class Man page
quadratic Man page
quadratic-class Man page
quadraticTransform Man page
randomFilterResult-class Man page
range Man page
range,flowFrame-method Man page
ratio Man page
ratio-class Man page
ratiotGml2 Man page
ratiotGml2-class Man page
rbind2,flowFrame,flowSet-method Man page
rbind2,flowSet,flowFrame-method Man page
rbind2,flowSet,flowSet-method Man page
rbind2,flowSet,flowSet,missing-method Man page
rbind2,flowSet,missing Man page
rbind2,flowSet,missing-method Man page
read.FCS Man page
read.FCSheader Man page
read.flowSet Man page
rectangleGate Man page
[,rectangleGate,ANY-method Man page
[,rectangleGate,character-method Man page
rectangleGate-class Man page
rectangleGate,filter-class Man page
*,rectangleGate,rectangleGate-method Man page
Rm Man page
Rm,actionItem,workFlow,character-method Man page
Rm,character,workFlow,character-method Man page
Rm,compensateActionItem,workFlow,character-method Man page
Rm,compensateView,workFlow,character-method Man page
Rm,fcNullReference,missing,character-method Man page
Rm,fcReference,missing,character-method Man page
Rm,fcReference,workFlow,character-method Man page
Rm,gateActionItem,workFlow,character-method Man page
Rm,gateView,workFlow,character-method Man page
Rm,normalizeActionItem,workFlow,character-method Man page
Rm,normalizeView,workFlow,character-method Man page
Rm,subsettingActionItem,workFlow,character-method Man page
Rm,subsettingView,workFlow,character-method Man page
Rm,transformActionItem,workFlow,character-method Man page
Rm,transformView,workFlow,character-method Man page
Rm,view,workFlow,character-method Man page
sampleFilter Man page
sampleFilter-class Man page
sampleNames<-,flowSet,ANY-method Man page
sampleNames,flowSet-method Man page
scaleTransform Man page
setOperationFilter-class Man page
show,boundaryFilter-method Man page
show,compensateActionItem-method Man page
show,compensation-method Man page
show,complementFilter-method Man page
show,ellipsoidGate-method Man page
show,expressionFilter-method Man page
show,fcNullReference-method Man page
show,fcReference-method Man page
show,filterList-method Man page
show,filter-method Man page
show,filterReference-method Man page
show,filterResultList-method Man page
show,filterResult-method Man page
show,filterSet-method Man page
show,filtersList-method Man page
show,filters-method Man page
show,filterSummary-method Man page
show,flowFrame-method Man page
show,flowSet-method Man page
show,gateActionItem-method Man page
show,intersectFilter-method Man page
show,kmeansFilter-method Man page
show,manyFilterResult-method Man page
show,multipleFilterResult-method Man page
show,norm2Filter-method Man page
show,normalizeActionItem-method Man page
show,polygonGate-method Man page
show,polytopeGate-method Man page
show,quadGate-method Man page
show,rectangleGate-method Man page
show,sampleFilter-method Man page
show,subsetFilter-method Man page
show,subsettingActionItem-method Man page
show,subsetting-method Man page
show,timeFilter-method Man page
show,transformActionItem-method Man page
show,transformFilter-method Man page
show,transformMap-method Man page
show,transform-method Man page
show,unionFilter-method Man page
show,unitytransform-method Man page
show,view-method Man page
show,workFlow-method Man page
singleParameterTransform-class Man page
sinht Man page
sinht-class Man page
sort,filterSet-method Man page
spillover Man page
spillover,flowFrame-method Man page
spillover,flowSet-method Man page
split Man page
split,flowFrame,ANY-method Man page
split,flowFrame,character-method Man page
split,flowFrame,factor-method Man page
split,flowFrame,filter-method Man page
split,flowFrame,filterSet-method Man page
split,flowFrame,logicalFilterResult-method Man page
split,flowFrame,manyFilterResult-method Man page
split,flowFrame,multipleFilterResult-method Man page
split,flowFrame,numeric-method Man page
split,flowSet,ANY-method Man page
split,flowSet,character-method Man page
split,flowSet,factor-method Man page
split,flowSet,filter-method Man page
split,flowSet,filterResultList-method Man page
split,flowSet,filterResult-method Man page
split,flowSet,list-method Man page
split,flowSet,numeric-method Man page
split-methods Man page
splitscale Man page
splitscale-class Man page
splitScaleTransform Man page
squareroot Man page
squareroot-class Man page
\%subset\% Man page
Subset Man page
\%subset\%,ANY-method Man page
subsetFilter-class Man page
\%subset\%,filter,filter-method Man page
subsetFilter-method Man page
\%subset\%,filterSet,filter-method Man page
Subset,flowFrame,filter-method Man page
Subset,flowFrame,logical-method Man page
Subset,flowFrame-method Man page
Subset,flowSet,ANY Man page
Subset,flowSet,ANY-method Man page
Subset,flowSet,filterResultList-method Man page
Subset,flowSet,list-method Man page
\%subset\%,list,filter-method Man page
subsetting Man page
subsettingActionItem Man page
subsettingActionItem-class Man page
subsetting-class Man page
subsettingView Man page
subsettingView-class Man page
summarizeFilter Man page
summarizeFilter,filterResult,filter-method Man page
summarizeFilter,filterResult,filterReference-method Man page
summarizeFilter,filterResult,parameterFilter-method Man page
summarizeFilter,filterResult,subsetFilter-method Man page
summarizeFilter,logicalFilterResult,norm2Filter-method Man page
summarizeFilter,logicalFilterResult,parameterFilter-method Man page
summarizeFilter-methods Man page
summarizeFilter,multipleFilterResult,parameterFilter-method Man page
summary,filter-method Man page
summary,filterReference-method Man page
summary,filterResultList-method Man page
summary,filterResult-method Man page
summary,flowFrame-method Man page
summary,flowSet-method Man page
summary,gateActionItem-method Man page
summary,gateView-method Man page
summary,logicalFilterResult-method Man page
summary,manyFilterResult-method Man page
summary,multipleFilterResult-method Man page
summary,rectangleGate-method Man page
summary,subsetFilter-method Man page
summary,transform-method Man page
summary,workFlow-method Man page
tail,flowFrame-method Man page
timeFilter Man page
timeFilter-class Man page
timeFilter-class Man page
toTable Man page
toTable,filterSummaryList-method Man page
toTable,filterSummary-method Man page
transform Man page
transformActionItem Man page
transformActionItem-class Man page
transformation-class Man page
transform-class Man page
transformFilter Man page
transformFilter-class Man page
transform,flowFrame-method Man page
transform,flowSet-method Man page
transformList Man page
transformList-class Man page
transformMap Man page
transformMap-class Man page
transform,missing-method Man page
transformReference Man page
transformReference-class Man page
transformView Man page
transformView-class Man page
tree Man page
tree,environment-method Man page
tree,workFlow-method Man page
truncateTransform Man page
undo Man page
unionFilter-class Man page
unitytransform Man page
unitytransform-class Man page
validFilters Man page
varLabels<-,flowSet,ANY-method Man page
varLabels<-,flowSet-method Man page
varLabels,flowSet-method Man page
varMetadata<-,flowSet,ANY-method Man page
varMetadata,flowSet-method Man page
view Man page
view-class Man page
views Man page
views,workFlow-method Man page
workFlow Man page
[,workFlow,ANY-method Man page
[[,workFlow,ANY-method Man page
workFlow-class Man page
$,workFlow-method Man page
write.FCS Man page
write.flowSet Man page
xyplot,formula,gateView-method Man page
xyplot,formula,view-method Man page
xyplot,view,missing-method Man page

Files

flowCore/DESCRIPTION
flowCore/NAMESPACE
flowCore/R
flowCore/R/AllClasses.R flowCore/R/AllGenerics.R flowCore/R/FCSTransTransform.R flowCore/R/IO.R flowCore/R/RcppExports.R flowCore/R/Rm-methods.R flowCore/R/actionItem-accessors.R flowCore/R/coerce.R flowCore/R/eval-methods.R flowCore/R/fcReference-accessors.R flowCore/R/filterResult-accessors.R flowCore/R/filterResultList-accessors.R flowCore/R/filterSet-accessors.R flowCore/R/filterSummary-accessors.R flowCore/R/flowFrame-accessors.R flowCore/R/flowSet-accessors.R flowCore/R/gatingML.R flowCore/R/identifier-methods.R flowCore/R/in-methods.R flowCore/R/initialize-methods.R flowCore/R/length-methods.R flowCore/R/logicalFilterResult-accessors.R flowCore/R/manyFilterResult-accessors.R flowCore/R/median-logicle-transform.R flowCore/R/multipleFilterResult-accessors.R flowCore/R/names-methods.R flowCore/R/on-methods.R flowCore/R/parameters-methods.R flowCore/R/rectangleGate-accessors.R flowCore/R/show-methods.R flowCore/R/split-methods.R flowCore/R/summarizeFilter-methods.R flowCore/R/summary-methods.R flowCore/R/transformList-accessors.R flowCore/R/utils.R flowCore/R/view-accessors.R flowCore/R/workFlow-accessors.R
flowCore/README.md
flowCore/build
flowCore/build/vignette.rds
flowCore/data
flowCore/data/GvHD.rda
flowCore/data/datalist
flowCore/examples
flowCore/examples/example1.r
flowCore/examples/example2.R
flowCore/hyperlog.notice.html
flowCore/inst
flowCore/inst/NEWS
flowCore/inst/doc
flowCore/inst/doc/HowTo-flowCore.R
flowCore/inst/doc/HowTo-flowCore.Rnw
flowCore/inst/doc/HowTo-flowCore.pdf
flowCore/inst/extdata
flowCore/inst/extdata/0877408774.B08
flowCore/inst/extdata/0877408774.E07
flowCore/inst/extdata/0877408774.F06
flowCore/inst/extdata/compdata
flowCore/inst/extdata/compdata/compmatrix
flowCore/inst/extdata/compdata/data
flowCore/inst/extdata/compdata/data/060909.001
flowCore/inst/extdata/compdata/data/060909.002
flowCore/inst/extdata/compdata/data/060909.003
flowCore/inst/extdata/compdata/data/060909.004
flowCore/inst/extdata/compdata/data/060909.005
flowCore/inst/scripts
flowCore/inst/scripts/smoothScatter
flowCore/inst/scripts/smoothScatter/backcol.jpg
flowCore/inst/scripts/smoothScatter/backgray.jpg
flowCore/inst/scripts/smoothScatter/backhue.jpg
flowCore/inst/scripts/smoothScatter/backsat.jpg
flowCore/inst/scripts/smoothScatter/backval.jpg
flowCore/inst/scripts/smoothScatter/blendFuns.R
flowCore/inst/scripts/smoothScatter/examples.R
flowCore/inst/scripts/smoothScatter/foreground.jpg
flowCore/inst/scripts/smoothScatter/smoothScatterMult.R
flowCore/inst/scripts/smoothScatter/testBlendEBImage.R
flowCore/inst/tests
flowCore/inst/unitTests
flowCore/man
flowCore/man/EHtrans-class.Rd flowCore/man/FCSTransTransform.Rd flowCore/man/GvHD.Rd flowCore/man/Subset-methods.Rd flowCore/man/actionItem-class.Rd flowCore/man/arcsinhTransform.Rd flowCore/man/asinht-class.Rd flowCore/man/asinhtGml2-class.Rd flowCore/man/biexponentialTransform.Rd flowCore/man/boundaryFilter-class.Rd flowCore/man/characterOrTransformation-class.Rd flowCore/man/checkOffset.Rd flowCore/man/coerce.Rd flowCore/man/compensateActionItem-class.Rd flowCore/man/compensateView-class.Rd flowCore/man/compensatedParameter-class.Rd flowCore/man/compensation-class.Rd flowCore/man/concreteFilter-class.Rd flowCore/man/dg1polynomial-class.Rd flowCore/man/each_col-methods.Rd flowCore/man/ellipsoidGate.Rd flowCore/man/estimateMedianLogicle.Rd flowCore/man/exponential-class.Rd flowCore/man/expressionFilter-class.Rd flowCore/man/fcReference-class.Rd flowCore/man/filter-and-methods.Rd flowCore/man/filter-class.Rd flowCore/man/filter-in-methods.Rd flowCore/man/filter-methods.Rd flowCore/man/filter-on-methods.Rd flowCore/man/filterDetails-methods.Rd flowCore/man/filterList-class.Rd flowCore/man/filterReference-class.Rd flowCore/man/filterResult-class.Rd flowCore/man/filterResultList-class.Rd flowCore/man/filterSet-class.Rd flowCore/man/filterSummary-class.Rd flowCore/man/filterSummaryList-class.Rd flowCore/man/filters-class.Rd flowCore/man/flowCore-package.Rd flowCore/man/flowFrame-class.Rd flowCore/man/flowSet-class.Rd flowCore/man/fsApply.Rd flowCore/man/gateActionItem-class.Rd flowCore/man/gateView-class.Rd flowCore/man/getChannelMarker.Rd flowCore/man/getIndexSort-methods.Rd flowCore/man/hyperlog-class.Rd flowCore/man/hyperlogtGml2-class.Rd flowCore/man/identifier-methods.Rd flowCore/man/inverseLogicleTransform.Rd flowCore/man/invsplitscale-class.Rd flowCore/man/keyword-methods.Rd flowCore/man/kmeansFilter.Rd flowCore/man/linearTransform.Rd flowCore/man/lintGml2-class.Rd flowCore/man/lnTransform.Rd flowCore/man/logTransform.Rd flowCore/man/logarithm-class.Rd flowCore/man/logicalFilterResult-class.Rd flowCore/man/logicleTransform.Rd flowCore/man/logicletGml2-class.Rd flowCore/man/logtGml2-class.Rd flowCore/man/manyFilterResult-class.Rd flowCore/man/markernames.Rd flowCore/man/multipleFilterResult-class.Rd flowCore/man/norm2Filter-class.Rd flowCore/man/normalization-class.Rd flowCore/man/normalizeActionItem-class.Rd flowCore/man/normalizeView-class.Rd flowCore/man/parameterFilter-class.Rd flowCore/man/parameterTransform-class.Rd flowCore/man/parameters-class.Rd flowCore/man/parameters-methods.Rd flowCore/man/polygonGate.Rd flowCore/man/polytopeGate.Rd flowCore/man/quadGate.Rd flowCore/man/quadratic-class.Rd flowCore/man/quadraticTransform.Rd flowCore/man/randomFilterResult-class.Rd flowCore/man/ratio-class.Rd flowCore/man/ratiotGml2-class.Rd flowCore/man/read.FCS.Rd flowCore/man/read.FCSheader.Rd flowCore/man/read.flowSet.Rd flowCore/man/rectangleGate.Rd flowCore/man/sampleFilter-class.Rd flowCore/man/scaleTransform.Rd flowCore/man/setOperationFilter-class.Rd flowCore/man/singleParameterTransform-class.Rd flowCore/man/sinht-class.Rd flowCore/man/spillover-flowSet.Rd flowCore/man/split-methods.Rd flowCore/man/splitScaleTransform.Rd flowCore/man/splitscale-class.Rd flowCore/man/squareroot-class.Rd flowCore/man/subsetting-class.Rd flowCore/man/subsettingActionItem-class.Rd flowCore/man/subsettingView-class.Rd flowCore/man/summarizeFilter-methods.Rd flowCore/man/timeFilter-class.Rd flowCore/man/transform-class.Rd flowCore/man/transformActionItem-class.Rd flowCore/man/transformFilter-class.Rd flowCore/man/transformList-class.Rd flowCore/man/transformMap-class.Rd flowCore/man/transformReference-class.Rd flowCore/man/transformView-class.Rd flowCore/man/transformation-class.Rd flowCore/man/truncateTransform.Rd flowCore/man/unitytransform-class.Rd flowCore/man/validFilters.Rd flowCore/man/view-class.Rd flowCore/man/workFlow-class.Rd flowCore/man/write.FCS.Rd flowCore/man/write.flowSet.Rd
flowCore/paper
flowCore/paper/Figure1-flowCoreFrameWork.jpg
flowCore/paper/Figure1.ppt
flowCore/paper/Figure2-flowWheel-version4.jpg
flowCore/paper/bmc_article.bib
flowCore/paper/bmc_article.bst
flowCore/paper/bmc_article.cls
flowCore/paper/bmc_article.tex
flowCore/paper/figure.R
flowCore/paper/flowCoreRef.bib
flowCore/paper/flowQ.jpg
flowCore/paper/manuscript.tex
flowCore/paper/outline.tex
flowCore/paper/response2reviewers.rtf
flowCore/paper/xyplot.pdf
flowCore/src
flowCore/src/FastLogicle.cpp
flowCore/src/Hyperlog.cpp
flowCore/src/Logicle.cpp
flowCore/src/Makevars
flowCore/src/RcppExports.cpp
flowCore/src/biexponential.cpp
flowCore/src/boost_regex
flowCore/src/boost_regex/README
flowCore/src/boost_regex/c_regex_traits.cpp
flowCore/src/boost_regex/c_regex_traits.o
flowCore/src/boost_regex/cpp_regex_traits.cpp
flowCore/src/boost_regex/cpp_regex_traits.o
flowCore/src/boost_regex/cregex.cpp
flowCore/src/boost_regex/cregex.o
flowCore/src/boost_regex/fileiter.cpp
flowCore/src/boost_regex/fileiter.o
flowCore/src/boost_regex/icu.cpp
flowCore/src/boost_regex/icu.o
flowCore/src/boost_regex/instances.cpp
flowCore/src/boost_regex/instances.o
flowCore/src/boost_regex/internals.hpp
flowCore/src/boost_regex/posix_api.cpp
flowCore/src/boost_regex/posix_api.o
flowCore/src/boost_regex/regex.cpp
flowCore/src/boost_regex/regex.o
flowCore/src/boost_regex/regex_debug.cpp
flowCore/src/boost_regex/regex_debug.o
flowCore/src/boost_regex/regex_raw_buffer.cpp
flowCore/src/boost_regex/regex_raw_buffer.o
flowCore/src/boost_regex/regex_traits_defaults.cpp
flowCore/src/boost_regex/regex_traits_defaults.o
flowCore/src/boost_regex/static_mutex.cpp
flowCore/src/boost_regex/static_mutex.o
flowCore/src/boost_regex/usinstances.cpp
flowCore/src/boost_regex/usinstances.o
flowCore/src/boost_regex/w32_regex_traits.cpp
flowCore/src/boost_regex/w32_regex_traits.o
flowCore/src/boost_regex/wc_regex_traits.cpp
flowCore/src/boost_regex/wc_regex_traits.o
flowCore/src/boost_regex/wide_posix_api.cpp
flowCore/src/boost_regex/wide_posix_api.o
flowCore/src/boost_regex/winstances.cpp
flowCore/src/boost_regex/winstances.o
flowCore/src/convertRawBytes.cpp
flowCore/src/convertRawBytes.h
flowCore/src/fcsTextParse.cpp
flowCore/src/flowCore_types.h
flowCore/src/hyperlog.h
flowCore/src/hyperlogTransform.cpp
flowCore/src/inPolygon.cpp
flowCore/src/inPolytope.cpp
flowCore/src/logicle.h
flowCore/src/logicleTransform.cpp
flowCore/src/pairVectorRcppWrap.cpp
flowCore/src/pairVectorRcppWrap.h
flowCore/src/sortBytes.cpp
flowCore/src/uint2double.cpp
flowCore/src/zeroin.cpp
flowCore/src/zeroin.h
flowCore/tests
flowCore/tests/testthat
flowCore/tests/testthat.R
flowCore/tests/testthat/IO-testSuite.R
flowCore/tests/testthat/expectResults.rds
flowCore/tests/testthat/helper-expectResults.R
flowCore/tests/testthat/test-classes.R
flowCore/tests/testthat/test-convertRawBytes.R
flowCore/tests/testthat/test-fcsTextParse.R
flowCore/tests/testthat/test-filter.R
flowCore/tests/testthat/test-flowSet-IO.R
flowCore/tests/testthat/test-gating.R
flowCore/tests/testthat/test-markernames.R
flowCore/tests/testthat/test-paramMatch.R
flowCore/tests/testthat/test-sortBytes.R
flowCore/tests/testthat/test-transform.R
flowCore/unitTests
flowCore/unitTests/InOutEventsTests
flowCore/unitTests/InOutEventsTests/ExpectedResult_Files
flowCore/unitTests/InOutEventsTests/FCS_Files
flowCore/unitTests/InOutEventsTests/Gating-ML_Files
flowCore/unitTests/InOutEventsTests/RUnitScript_Files
flowCore/unitTests/InvalidGateTests
flowCore/unitTests/InvalidGateTests/FCS_Files
flowCore/unitTests/InvalidGateTests/Gating-ML_Files
flowCore/unitTests/InvalidGateTests/RUnitScript_Files
flowCore/unitTests/ValidGateTests
flowCore/unitTests/ValidGateTests/Gating-ML_Files
flowCore/vignettes
flowCore/vignettes/HowTo-flowCore.Rnw
flowCore/vignettes/cytoref.bib
flowCore/vignettes/fcs3.html

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