Man pages for xu-lab/SINCERA
An R implementation of SINCERA pipeline for processing single-cell RNA-seq data.

batch.analysisAnalyzing batch difference
batch.analysis.ISCCDAnalyze the inter-sample correlation and distance
batch.analysis.MAplot the MA plot for two sets of cells
batch.analysis.QQplot the QQ plot for two sets of cells
celltype.enrichmentPerform cell type enrichment
celltype.enrichment.initKBContruct the knowledge base for cell type enrichment analysis
celltype.validationPerforming rank-aggregation based cell type validation using...
cluster.assignmentPartition cells into disjoint clusters
cluster.diffgenesDetect cluster specific differentially expressed genes
cluster.geneSelectionSelecting genes for cell cluster identification
clusterings.compareCompare and visualze multiple clustering assignments
cluster.orderingOrdering rows or columns according to a specified order
cluster.permutation.analysisValidating clustering results using permutation analysis
cluster.permutation.analysis.1Permutation Analysis for determining significance of cluster...
consensus_maximizationconsensus maximization
constructConstruct a sincera object
copyCellMetaAdd or update a cell meta data using a predefined cell meta...
copyGeneMetaAdd or update a gene meta data using a predefined gene meta...
doPCAPerform PCA based dimension reduction
doTSNEPerform tSNE based dimension reduction
drivingforce.getLCCExtract largest connected component (LCC) of the cell group...
drivingforce.inferTRNInferring significant TF->TF and TF->TG interactions based on...
drivingforce.rankTFsRank TFs based on their importance to the LCC measured by six...
drivingforce.selectTFsSelect candidate TFs for network inference and TF ranking
drivingforce.selectTGsSelect candidate TGs for network inference and TF ranking
expr.minimumSet the lower bound of gene expression
exprs.commonIdentifying group specific common genes
exprs.specificityPer group expression specificity calculation
exprs.synthetic.similarityCalculating the similarity between each gene profile and...
exprs.test.statistic.metricNormalized and smoothened results of group specific...
exprs.uniqueIdentifying group specific unique genes
filterContaminatedCellsDetecting and removing potentially contaminated cells
filterLowQualityCellspre-filtering low quality cells
GeneStatsGenerate gene level global or per group statistics
getCellMetaGet the meta data of cells in a sincera object
getCellNumGet the number of cells in a sincera object
getCellsget the names of cells in specified cell groups in a sincera...
getCellTypeGet the cell types of given cell groups
getCellTypeMarkersGet cell type marker information defined in a sincera object
getExpressionget expression matrix from a sincera object
getExprQuantilesGet and plot the quantiles of gene expression per cell
getGeneMetaGet a gene meta data
getGeneNumGet the number of the genes in a sincera object
getGenesGet the names of all genes in a sincera object
getGenesForClusteringGet the set of genes used for cell cluster identification
getNodesImportanceCalculate the importance of a node in a graph
getPCAGet the PCA results stored in a sincera object
helloHello, World!
network.inferenceInferring first order conditional dependencies between TFs...
normalization.loglog transformation
normalization.sqrtsquare root transformation
normalization.trimmed.meanTrimmed mean normalization
normalization.zscorePerforming zscore scaling of gene expression
normalization.zscore.1Per group zscore normalization of gene expression profiles
plotCellTypeEnrichmentBarplot of the cell type enrichment results
plotHCPlot the dendrogram tree of hierarchical clustering
plotHeatmapPlot heatmap
plotMarkersPlot gene expression patterns
plotPCASDPlot the standard deviation of principal components
plotRDS2D plot of cells in the PCA or tSNE reduced dimensional...
prefilterGenesPre-filtering genes with low abundancy
setCellMetaAdd or update meta data of cells in a sincera object
setCellNamesset the names of all cells in a sincera object
setCellTypeMap cell clusters to cell types
setCellTypeMarkersAdd cell type marker information into sincera
setExpressionUpdate expression matrix in a sincera object
setGeneMetaAdd or update meta data of genes in a sincera object
setGeneNamesUpdate the gene names in a sincera object
setGenesForClusteringUpdate the set of genes used for cell cluster identification
setPCAUpdate the PCA results in sincera
signature.predictionPredicting cell type signature
signature.prediction.1logistic regression based signature prediction and cross...
signature.validationValidating cell type signature using random subsampling mehod
sigpred.testing.setsConstructing group specific testing sets for signature...
sigpred.training.setsConstructing group specific training sets for signature...
sinceraThe sincera Class
specificity.criterion.selectionDetermine the threshold for specificity filter based on a set...
specificity.thresholdSelectionSelecting a threshold value for specificity
xu-lab/SINCERA documentation built on July 26, 2017, 9:04 p.m.