Man pages 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

adjustAccordingToFractionsadjustAccordingToFractions
adjustFractionsadjustFractions
appropriateSingletsappropriateSinglets
calcResidualscalcResiduals
calculateCostcalculateCost
calculateCostDensitycalculateCostDensity
calculateCostscalculateCosts
calculateEdgeStatscalculateEdgeStats
calculateLogRowMeanscalculateLogRowMeans
cellNumberPerClasscellNumberPerClass
CIMseqMultipletsCIMseqMultiplets
CIMseqMultiplets_testCIMseqMultiplets object corresponding to test dataset.
CIMseq-packageA package for analyzing tissue spatiality in scRNAseq data.
CIMseqSingletsCIMseqSinglets
CIMseqSinglets_testCIMseqSinglets object corresponding to test dataset.
CIMseqSwarmCIMseqSwarm
CIMseqSwarm_testCIMseqSwarm object corresponding to test dataset.
classify_louvainclassify_louvain
col40col40
coloursFromTargetscoloursFromTargets
constructGraphconstructGraph
convertToERCCconvertToERCC
costcost
costCalccostCalc
costNegSumcostNegSum
countsPerClasscountsPerClass
divide_bydivide_by
draw_legenddraw_legend
erccPerClasserccPerClass
estimateCellsestimateCells
estimateTotalConnectionsestimateTotalConnections
expectedInteractionFreqexpectedInteractionFreq
fixNegInffixNegInf
getCellsForMultipletgetCellsForMultiplet
getEdgesForMultipletgetEdgesForMultiplet
getKNNgetKNN
getMultipletsForEdgegetMultipletsForEdge
gg-class"gg" class
g_legendg_legend
jaccardSimilarityjaccardSimilarity
longFormConnectionslongFormConnections
matrix_to_tibblematrix_to_tibble
means.dim.redmeans.dim.red
multipletSumsmultipletSums
multiply_bymultiply_by
namedListToTibblenamedListToTibble
normalizeFractionsnormalizeFractions
normalizeVecnormalizeVec
pcByVarPercentpcByVarPercent
pearsonsDistpearsonsDist
plotCountsDataplotCountsData
plotCountsERCCplotCountsERCC
plotCountsMarkersplotCountsMarkers
plotDataplotData
plotSwarmBarBaseplotSwarmBarBase
plotSwarmCircosplotSwarmGenes
plotSwarmEdgeBarplotSwarmEdgeBar
plotSwarmGenesplotSwarmGenes
plotSwarmGraphplotSwarmGraph
plotSwarmHeatplotSwarmHeat
plotSwarmPbarplotSwarmPbar
plotSwarmPositionplotSwarmPosition
plotUnsupervisedClassplotUnsupervisedClass
plotUnsupervisedMarkersplotUnsupervisedMarkers
processMarkersprocessMarkers
removeOutliersremoveOutliers
runPCArunPCA
runTsnerunTsne
sampleSingletssampleSinglets
selectTopMaxselectTopMax
selectTopVarselectTopVar
subsetSingletssubsetSinglets
testCountsCounts data used to demonstrate CIMseq package.
testMetaMeta data for the testCounts dataset.
tidySingletstidySinglets
tidySwarmtidySwarm
vecToMatvecToMat
jasonserviss/CIMseq documentation built on May 8, 2019, 9:55 p.m.