API for nukappa/seurat_v2
Seurat : R toolkit for single cell genomics

Global functions
AddImputedScore Man page
AddMetaData Man page
AddSamples Man page
AddSmoothedScore Man page
AssessNodes Man page
AssessSplit Man page
AverageExpression Man page
AveragePCA Man page
BatchGene Man page
BuildClusterTree Man page
BuildRFClassifier Man page
BuildSNN Man page
CalcConnectivity Source code
CalcSNNDense Source code
CalcSNNSparse Source code
CellPlot Man page
ClassifyCells Man page
ClusterAlpha Man page
ColorTSNESplit Man page
DBClustDimension Man page
DBclust_dimension Man page Source code
DFT Source code
DiffExpTest Man page
DiffTTest Man page
DimPlot Man page
DoHeatmap Man page
DoKMeans Man page
DotPlot Man page
FeatureHeatmap Man page
FeaturePlot Man page
FetchData Man page
FindAllMarkers Man page
FindAllMarkersNode Man page
FindClusters Man page
FindMarkers Man page
FindMarkersNode Man page
FitGeneK Man page
GenePlot Man page
GetAllInternalNodes Source code
GetCentroids Man page
GroupSingletons Source code
Hbeta Source code
HeatmapNode Man page
ICA Man page
ICAPlot Man page
ICHeatmap Man page
ICTopGenes Man page
InitialMapping Man page
JackStraw Man page
JackStrawPlot Man page
KClustDimension Man page
Kclust_dimension Man page Source code
KullbackFun Source code
LogNorm Source code
LogNormalize Man page
MakeSparse Man page
MarkerTest Man page
MeanVarPlot Man page
MergeNode Man page
MergeSeurat Man page
MultiPlotList Source code
NegBinomDETest Man page
NegBinomDiffExpTest Source code
NodeHasChild Source code
NodeHasOnlyChildren Source code
PCA Man page
PCAFast Man page
PCAPlot Man page
PCASigGenes Man page
PCElbowPlot Man page
PCHeatmap Man page
PCTopCells Man page
PCTopGenes Man page
PlotClusterTree Man page
PlotNoiseModel Man page
PoissonDETest Man page
PrintPCA Man page
ProjectPCA Man page
Read10X Man page
RefinedMapping Man page
RegressOut Man page
RenameIdent Man page
ReorderIdent Man page
RowMergeMatrices Source code
RowMergeSparseMatrices Source code
RunClassifier Source code
RunDiffusion Man page
RunModularityClustering Source code
RunTSNE Man page
RunUMISampling Source code
RunUMISamplingPerCell Source code
SampleUMI Man page
ScaleData Man page
SetAllIdent Man page
SetIdent Man page
Setup Man page
Seurat-deprecated Man page
SingleFeaturePlot Source code
StashIdent Man page
SubsetCells Man page
SubsetData Man page
TSNEPlot Man page
TobitDiffExpTest Source code
TobitTest Man page
ValidateClusters Man page
ValidateSpecificClusters Man page
VizClassification Man page
VizICA Man page
VizPCA Man page
VlnPlot Man page
WhichCells Man page
addImputedScore Man page Source code
addMetaData Man page Source code
addSmoothedScore Man page Source code
add_samples Man page Source code
ainb Source code
all.neighbor.cells Source code
anotinb Source code
arrange Source code
auc Source code
aucFxn Source code
average.expression Man page Source code
average.pca Man page Source code
batch.gene Man page Source code
bimodLikData Source code
buildClusterTree Man page Source code
calc.drop.prob Source code
calc.insitu Man page Source code
calcFP Source code
calcMedians Source code
calcNoiseModels Man page Source code
calcResid Source code
calcResidLog Source code
calcTP Source code
calinskiPlot Man page Source code
cell.centroid Source code
cell.centroid.x Source code
cell.centroid.y Source code
cell.cor.matrix Man page Source code
cellPlot Man page Source code
cluster.alpha Man page Source code
compareBins Source code
comparePCA Source code
corCellWeightFast Source code
covCellWeightFast Source code
custom.dist Source code
cv Source code
d2p_cell Source code
debugdmvnorm Source code
diff.t.test Man page Source code
diffAUC Source code
diffExp.test Man page Source code
diffLRT Source code
diffNegBinom Source code
diffTobit Source code
dim.plot Man page Source code
doHeatMap Man page Source code
doKMeans Man page Source code
dot.plot Man page Source code
empP Source code
exact.cell.centroid Source code
expAlpha Source code Source code
expMean Source code
expSD Source code
expVar Source code
extract_field Source code
feature.heatmap Man page Source code
feature.plot Man page Source code
feature.plot.keynote Man page Source code
fetch.closest Source code
fetch.data Man page Source code
fetch.mincells Source code
find.markers Man page Source code
find.markers.node Man page Source code
findNGene Source code
find_all_markers Man page Source code
fit.gene.k Man page Source code
fit.gene.mix Man page Source code
genCols Source code
gene.cor.matrix Man page Source code
genePlot Man page Source code
geneScorePlot Man page Source code
genes.ca.range Source code
genes.in.cluster Man page Source code
get.centroids Man page Source code
getAB Source code
getCoefs Source code
getDescendants Source code
getLeftDecendants Source code
getNewScore Man page Source code
getRightDecendants Source code
getSmooth Source code
getStat Source code
getStat1 Source code
getStat2 Source code
getStat3 Source code
getWeightMatrix Man page Source code
gg.legend.pts Source code
gg.legend.text Source code
gg.xax Source code
gg.yax Source code
gtCut Source code
heatmap2NoKey Source code
humpCt Source code
humpMean Source code
humpVar Source code
icHeatmap Man page Source code
icTopGenes Man page Source code
ica Man page Source code
ica.plot Man page Source code
init Source code
initial.mapping Man page Source code
iter.k.fit Source code
jackF Source code
jackRandom Source code
jackStraw Man page Source code
jackStraw.permutation.test Man page Source code
jackStrawF Source code
jackStrawFull Man page Source code
jackStrawMC Man page Source code
jackStrawPlot Man page Source code
kMeansHeatmap Man page Source code
kill.ifnull Source code
lasso.fxn Source code
logMeanMinus Source code
logVarDivMean Source code
logVarMinus Source code
logVarMinus2 Source code
log_add Source code
makeAlnPlot Source code
makeScorePlot2 Source code
map.cell Man page Source code
map.cell.score Source code
marker.auc.test Source code
marker.test Man page Source code
mean.var.plot Man page Source code
meanNormFunction Source code
meanVarPlot Source code
mergeDescendents Source code
minmax Source code
minusc Source code
minusr Source code
myPalette Source code
nb.residuals Source code
neighbor.cells Source code
normal.sample Source code
pcHeatmap Man page Source code
pcTopCells Man page Source code
pcTopGenes Man page Source code
pca Man page Source code
pca.plot Man page Source code
pca.sig.genes Man page Source code
plot.Vln Source code
plotClusterTree Man page Source code
plotNoiseModel Man page Source code
plotVln Source code
posterior.plot Man page Source code
print.pca Man page Source code
project.pca Man page Source code
project.samples Man page Source code
project_map Source code
quickRNAHuman Source code
refined.mapping Man page Source code
regression.sig Source code
regulatorScore Man page Source code
removePC Man page Source code
rename.ident Man page Source code
reorder.ident Man page Source code
returnTopX Source code
rp Source code
run_diffusion Man page Source code
run_tsne Man page Source code
same Source code
scaleSCMatrix2 Source code
sensitivityCurve Source code
set.all.ident Man page Source code
set.ident Man page Source code
set.ifnull Source code
setWt1 Source code
setWtMatrix1 Source code
setup Man page Source code
seurat Man page
seurat-class Man page
shift.cell Source code
shuffleMatRow Source code
situ3d Source code
slimdmvnorm Source code
slimdmvnorm_nosum Source code
sort.column Source code
spatial.de Man page Source code
sub.string Source code
subSort Source code
subc Source code
subr Source code
subsetCells Man page Source code
subsetData Man page Source code
tnse.plot Man page
tobit.test Man page Source code
tobit_fitter Source code
topGenesForDim Source code
translate.dim.code Source code
tsne.plot Man page Source code
viz.ica Man page Source code
viz.pca Man page Source code
vlnPlot Man page Source code
vminusc Source code
vp.layout Source code
vsubc Source code
weighted.euclidean Source code
which.cells Man page Source code
writ.table Source code
wtCov Source code
zf.anchor.map Source code
zf.anchor.render Source code
zf.cells.render Source code
zf.insitu.dorsal Source code
zf.insitu.lateral Source code
zf.insitu.side Source code
zf.insitu.vec.lateral Source code
zf.insitu.ventral Source code
nukappa/seurat_v2 documentation built on May 23, 2017, 5:26 p.m.