jasonserviss/CIMseq
CIMseq is a software suite for analysis of scRNAseq data that has been produced using the cellular interactions by multiplet sequencing method

Package index
Search the jasonserviss/CIMseq package
Vignettes
Functions
168
Source code
28
Man pages
69
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jasonserviss/CIMseq: CIMseq is a software suite for analysis of scRNAseq data that has been produced using the cellular interactions by multiplet sequencing method
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API

API for jasonserviss/CIMseq
CIMseq is a software suite for analysis of scRNAseq data that has been produced using the cellular interactions by multiplet sequencing method

Global functions
.checkCIMseqMultipletsReplacement Source code
.checkCIMseqSingletsReplacement Source code
.checkEstimateCellsInput Source code
.class_legend Source code
.closestCircle Source code
.ec Source code
.frac_legend Source code
.inputCheckMultiplets Source code
.inputCheckSinglets Source code
.norm.counts Source code
.norm.log.counts Source code
.ns_legend Source code
.obsexp_legend Source code
.pd Source code
.processSwarm Source code
.rc Source code
.showBasics Source code
.showCIMseqData Source code
.showCIMseqSwarm Source code
.showFunction Source code
.showList Source code
.showMatrix Source code
.showTibble Source code
CIMseq Man page
CIMseq-package Man page
CIMseqMultiplets Man page
CIMseqMultiplets,matrix-method Man page
CIMseqMultiplets,missing-method Man page
CIMseqMultiplets-class Man page
CIMseqMultiplets_test Man page
CIMseqSinglets Man page
CIMseqSinglets,matrix-method Man page
CIMseqSinglets,missing-method Man page
CIMseqSinglets-class Man page
CIMseqSinglets_test Man page
CIMseqSwarm Man page
CIMseqSwarm,CIMseqSinglets,CIMseqMultiplets-method Man page
CIMseqSwarm-class Man page
CIMseqSwarm_test Man page
adjustAccordingToFractions Man page Source code
adjustFractions Man page
appropriateSinglets Man page
c,CIMseqMultiplets-method Man page
c,CIMseqSinglets-method Man page
c,CIMseqSwarm-method Man page
calcResiduals Man page
calculateCost Man page Source code
calculateCostDensity Man page Source code
calculateCosts Man page
calculateCosts,CIMseqSinglets,CIMseqMultiplets,CIMseqSwarm-metho Man page
calculateEdgeStats Man page
calculateLogRowMeans Man page Source code
cellNumberPerClass Man page Source code
col40 Man page
coloursFromTargets Man page Source code
convertToERCC Man page Source code
cost Man page Source code
costCalc Man page Source code
costNegSum Man page Source code
countsPerClass Man page Source code
divide_by Man page
draw_legend Man page
erccPerClass Man page Source code
estimateCells Man page
estimateCells,CIMseqSinglets-method Man page
estimateTotalConnections Man page
expectedInteractionFreq Man page Source code
filterSwarm Man page
filterSwarm,CIMseqSwarm-method Man page
fixNegInf Man page Source code
g_legend Man page
getCellsForMultiplet Man page
getCellsForMultiplet,CIMseqSwarm-method Man page
getData Man page
getData,CIMseqMultiplets-method Man page
getData,CIMseqSinglets-method Man page
getData,CIMseqSwarm-method Man page
getData<- Man page
getData<-,CIMseqMultiplets-method Man page
getData<-,CIMseqSinglets-method Man page
getEdgesForMultiplet Man page
getEdgesForMultiplet,CIMseqSwarm-method Man page
getMultipletsForEdge Man page
getMultipletsForEdge,CIMseqSwarm-method Man page
gg Man page
gg-class Man page
ggraph Man page
ggraph-class Man page
initialize,CIMseqMultiplets-method Man page
initialize,CIMseqSinglets-method Man page
initialize,CIMseqSwarm-method Man page
longFormConnections Man page
matrix_to_tibble Man page Source code
means.dim.red Man page Source code
multipletSums Man page Source code
multiply_by Man page
namedListToTibble Man page Source code
normalizeFractions Man page Source code
normalizeVec Man page Source code
pearsonsDist Man page Source code
plotCountsData Man page
plotCountsData,CIMseqSinglets,CIMseqMultiplets-method Man page
plotCountsERCC Man page
plotCountsERCC,CIMseqSinglets,CIMseqMultiplets-method Man page
plotCountsMarkers Man page
plotCountsMarkers,CIMseqSinglets,CIMseqMultiplets-method Man page
plotData Man page
plotData,data.frame-method Man page
plotData,gg-method Man page
plotData,ggraph-method Man page
plotSwarmCircos Man page
plotSwarmCircos,CIMseqSwarm-method Man page
plotSwarmGenes Man page
plotSwarmGenes,CIMseqSwarm-method Man page
plotSwarmGraph Man page
plotSwarmGraph,CIMseqSwarm,CIMseqSinglets,CIMseqMultiplets-metho Man page
plotSwarmPosition Man page
plotSwarmPosition,CIMseqSwarm-method Man page
plotUnsupervisedClass Man page
plotUnsupervisedClass,CIMseqSinglets-method Man page
plotUnsupervisedMarkers Man page
plotUnsupervisedMarkers,CIMseqSinglets,CIMseqMultiplets-method Man page
processMarkers Man page
pso.2.0 Man page
runTsne Man page Source code
sampleSinglets Man page Source code
selectTopMax Man page Source code
selectTopVar Man page Source code
show,CIMseqMultiplets-method Man page
show,CIMseqSinglets-method Man page
show,CIMseqSwarm-method Man page
subsetSinglets Man page Source code
swarmInit Man page Source code
testCounts Man page
testMeta Man page
tidySinglets Man page Source code
tidySwarm Man page Source code
vecToMat Man page Source code
jasonserviss/CIMseq documentation built on Jan. 11, 2020, 4:42 a.m.

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