NMikolajewicz/scMiko
scRNAseq analysis functions. Developed using Seurat framework.

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NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.
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API

API for NMikolajewicz/scMiko
scRNAseq analysis functions. Developed using Seurat framework.

Global functions
AddSModuleScore Man page
LR.db Man page
QC.scatterPlot Man page Source code
QC.violinPlot Man page Source code
SSNConnectivity Man page Source code
SSNExpression Man page Source code
SSNResolution Man page Source code
addLogEntry Man page Source code
aggGroupExpression Man page Source code
annotationCloud Man page Source code
autoPointSize Man page Source code
avgGroupExpression Man page Source code
baderPathways Man page
balanceMatrixSize Man page Source code
balanceSamples Man page Source code
barcodeLabels Man page Source code
benchmarkCluster Man page Source code
benchmarkScores Man page Source code
categoricalColPal Man page Source code
checkGeneRep Man page Source code
citationCheck Man page Source code
cleanCluster Man page Source code
cleanFilterGenes Man page Source code
clearGlobalEnv Man page Source code
cluster.UMAP Man page Source code
clusterFilter Man page Source code
coherentFraction Man page Source code
col2rowname Man page Source code
consolidateNMF Man page Source code
da_DEG Man page Source code
da_Run Man page Source code
detectSpecies Man page Source code
dist2hclust Man page Source code
downsampleSeurat Man page Source code
eigengene Man page Source code
ens2sym.so Man page Source code
ensembl2sym Man page Source code
entrez2sym Man page Source code
exprUMAP Man page Source code
expression.Plot Man page Source code
featureGradient Man page Source code
filterSeurat Man page Source code
findArtifactGenes Man page Source code
findCDIMarkers Man page Source code
findConservedCDIMarkers Man page Source code
findCorMarkers Man page Source code
findGiniMarkers Man page Source code
findNetworkFeatures Man page Source code
firstup Man page Source code
fixBarcodeLabel Man page
flex.asDT Man page Source code
flex.multiTabLogs Man page Source code
flex.multiTabPlot Man page Source code
flex.multiTabPlotly Man page Source code
flex.multiTabTables Man page Source code
geneRepCurve Man page Source code
geneSets Man page
geom_split_violin Man page Source code
getAnnotationPathways Man page Source code
getClusterCenters Man page Source code
getConnectivity Man page Source code
getDEG Man page Source code
getDensity Man page Source code
getExpressedGenes Man page Source code
getExpressingCells Man page Source code
getExpressionMatrix Man page Source code
getICAGenes Man page Source code
getJaccard Man page Source code
getLoadPath Man page
getMitoContent Man page Source code
getModuleGenes Man page Source code
getModulePreservation Man page Source code
getNMFGenes Man page Source code
getNodesEdges Man page Source code
getOrderedGroups Man page Source code
getReductionGenes Man page Source code
getSoftThreshold Man page
getSoftThreshold2 Man page Source code
getUMAP Man page Source code
group2list Man page Source code
highlightUMAP Man page Source code
id2geneset Man page Source code
id2term Man page Source code
inferSpecies Man page Source code
inferState Man page Source code
initiateLog Man page
jaccardSimilarityMatrix Man page Source code
lintersect Man page Source code
loadCellRanger Man page Source code
loadMat Man page Source code
loadMoffat Man page Source code
longDF2namedList Man page Source code
mergeSeuratList Man page Source code
mikoScore Man page Source code
miko_heatmap Man page Source code
miko_integrate Man page Source code
miko_message Man page Source code
miko_volcano Man page Source code
multiCluster Man page Source code
multiSilhouette Man page Source code
multiSpecificity Man page Source code
namedList2longDF Man page Source code
namedList2wideDF Man page Source code
neighborPurity Man page Source code
netHG Man page Source code
nullScore Man page Source code
optimalBinSize Man page
optimalDS Man page Source code
orderedFactor Man page Source code
p2z Man page Source code
parCor Man page Source code
pcaElbow Man page Source code
prepGeneList Man page
prepSeurat Man page
prepSeurat2 Man page
projectReduction Man page Source code
propVarPCA Man page Source code
pruneSSN Man page Source code
pseudoReplicates Man page Source code
pseudotimeRF Man page Source code
qNorm Man page Source code
recodeBarcode Man page Source code
rescaleValues Man page Source code
rmDuplicateGenes Man page Source code
rmvCSVprefix Man page Source code
runAUC Man page Source code
runAUGUR Man page
runBBKNN Man page Source code
runGSEA Man page Source code
runHG Man page Source code
runICA Man page Source code
runMS Man page Source code
runNMF Man page Source code
runRPCA Man page Source code
runSSN Man page Source code
runScanorama Man page Source code
runWGCNA Man page Source code
saveHTML Man page Source code
savePDF Man page Source code
scExpression.UMAP Man page Source code
scMikoUpdate Man page Source code
scNormScale Man page Source code
scaleFreeNet Man page Source code
scaleTOM Man page Source code
scale_color_miko Man page Source code
scale_fill_miko Man page Source code
scoreGBM Man page Source code
scoreStem Man page
searchAnnotations Man page Source code
setResolution Man page Source code
sigScore Man page Source code
signatureCoherence Man page Source code
sim2adj Man page Source code
snip Man page Source code
sparse2dense Man page Source code
sparse2df Man page Source code
speciesConvert Man page Source code
springNet Man page Source code
subsetDimRed Man page Source code
subsetSeurat Man page
summarizeHG Man page Source code
summarizeModules Man page Source code
sym2ens Man page Source code
sym2entrez Man page Source code
term2id Man page Source code
theme_miko Man page Source code
ulength Man page Source code
uniqueFeatures Man page Source code
updateCentralLog Man page Source code
updateDimNames Man page Source code
updateGeneSets Man page Source code
upset.Plot Man page Source code
value2col Man page Source code
varExpPCA Man page Source code
variableGenes.Plot Man page Source code
vd_Formula Man page Source code
vd_Inputs Man page Source code
vd_Run Man page Source code
vd_UMAP Man page Source code
wgcna2graphDF Man page Source code
wideDF2namedList Man page Source code
wnn_Components Man page Source code
wnn_Run Man page
z2p Man page Source code
NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.

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