Man pages for Japrin/sscClust
simpler single cell RNAseq data clustering

auto.colSetGenerate color set automatically
auto.point.sizeDetermine point size automatically
binarizeExpbinarize the expression value using the distribution
classifyCell.by.sigGeneplot genes expression in pairs of clusters to examine the...
classify.outlieroutlier detection using extremevalues
cor.BLASCorrelation calculation. use BLAS and data.table to speed up.
expressedFractionFor each gene, calculate the frequency of cells in each...
expressedFraction.HiExpressorMeanFor each gene, calculate the average expression of the...
fftRtsneWraper for running FIt-SNE. Code from KlugerLab...
findDEGenesByAOVdifferential expression analysis
findKneePointFind the knee point of the scree plot
getAUCcalculate the AUC of one gene, using it as a classifier. code...
ggGeneOnTSNEPlot gene expression on tSNE map
integrate.by.avgintegrate dataset by calculating the average expression and...
loginfodispaly message with time stamp
matrix.waterfallmake the matrix looks like "waterfall" (typically genes...
plot.branchplot matrix (typically genes expression)
plot.density2DWrap for plotting 2D density
plotDistFromCellInfoTableplot distribution using cell info table
plot.matrix.simpleplot matrix (typically genes expression)
plot.pairs.corplot genes expression in pairs of clusters to examine the...
plotSigGeneplot signature genes
rank.de.geneget gene ranking table from obj
run.cutreeDynamicrun dynamicTreeCut::cutreeDynamic on rows of the given matrix
run.KNNWraper for running random forest classifier
run.limma.matrixrun limma, given an expression matrix
run.RFWraper for running random forest classifier
run.SC3Wraper for running SC3
run.SVMWraper for running svm
run.tSNEWraper for running Rtsne
sce.PollenSingle cell RNA-Seq data extracted from a publication by...
simple.removeBatchEffectModified from limma::removeBatchEffect, a little different...
ssc.assay.hclustsort by hierarchical clustering
ssc.assay.zscorescale the assay per gene
ssc.average.cellcalcualte the average expression of cells of each group
ssc.buildBuild an SingleCellExperiment object
ssc.clustPerform clustering using reduced data
ssc.clusterMarkerGeneidentify marker genes of each cluster
ssc.clustSubsamplingClassificationClustering with subsampling and classification
ssc.DEGene.limmaidentify differential genes of each cluster (comparing the...
ssc.displayName2idConvert display name (gene symbol) to gene id
ssc.downsampledownsample
ssc.id2displayNameConvert gene id to display name (gene symbol)
ssc.moduleScoreAdd module scores for gene expression programs in single...
ssc.orderorder genes and cells
ssc.plotGeneDensityplot gene expression density
ssc.plot.heatmapplot heatmap
ssc.plot.pcaPlot pca result, such as scree plot.
ssc.plot.silhouetteWraper for silhouette()
ssc.plot.tsnePlot on tSNE map
ssc.plot.violinPlot violin
ssc.reduceDimReduce dimension by various methods
ssc.runWrapper for running all the pipeline
ssc.scalescale the data
ssc.variableGeneIdentify variable genes
Japrin/sscClust documentation built on Nov. 7, 2019, 10:34 a.m.