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"cbind.ligerDataset", "dim,ligerDataset-method", "dimnames,ligerDataset-method", "dimnames<-,ligerDataset,list-method", "featureMeta", "featureMeta,ligerDataset-method", "featureMeta<-", "featureMeta<-,ligerDataset-method", "getH5File", "getH5File,ligerDataset,missing-method", "getMatrix", "getMatrix,ligerATACDataset,ANY,missing,missing-method", "getMatrix,ligerDataset,ANY,missing,missing-method", "h5fileInfo", "h5fileInfo,ligerDataset-method", "h5fileInfo<-", "h5fileInfo<-,ligerDataset-method", "ligerDataset", "ligerDataset-class", "normData", "normData,ligerDataset-method", "normData<-", "normData<-,ligerDataset,ANY,ANY,H5D-method", "normData<-,ligerDataset,ANY,ANY,matrixLike_OR_NULL-method", "rawData", "rawData,ligerDataset-method", "rawData<-", "rawData<-,ligerDataset,ANY,ANY,H5D-method", "rawData<-,ligerDataset,ANY,ANY,matrixLike_OR_NULL-method", "scaleData", "scaleData,ligerDataset,missing-method", "scaleData<-", "scaleData<-,ligerDataset,ANY,ANY,H5D-method", "scaleData<-,ligerDataset,ANY,ANY,H5Group-method", "scaleData<-,ligerDataset,ANY,ANY,matrixLike_OR_NULL-method", "scaleUnsharedData", "scaleUnsharedData,ligerDataset,missing-method", "scaleUnsharedData<-", "scaleUnsharedData<-,ligerDataset,missing,ANY,H5D-method", "scaleUnsharedData<-,ligerDataset,missing,ANY,H5Group-method", "scaleUnsharedData<-,ligerDataset,missing,ANY,matrixLike_OR_NULL-method", "show,ligerDataset-method" ] }, { "page": "ligerMethDataset-class", "title": "Subclass of ligerDataset for Methylation modality", "topics": [ "ligerMethDataset", "ligerMethDataset-class" ] }, { "page": "ligerRNADataset-class", "title": "Subclass of ligerDataset for RNA modality", "topics": [ "ligerRNADataset", "ligerRNADataset-class" ] }, { "page": "ligerSpatialDataset-class", "title": "Subclass of ligerDataset for Spatial modality", "topics": [ "ligerSpatialDataset", "ligerSpatialDataset-class" ] }, { "page": "ligerToSeurat", "title": "Convert between liger and Seurat object", "topics": [ "ligerToSeurat" ] }, { "page": "linkGenesAndPeaks", "title": "Linking genes to putative regulatory elements", "topics": [ "linkGenesAndPeaks" ] }, { "page": "louvainCluster-deprecated", "title": "*[Superseded]* Louvain algorithm for community detection", "topics": [ "louvainCluster-deprecated" ] }, { "page": "makeFeatureMatrix", "title": "Fast calculation of feature count matrix", "topics": [ "makeFeatureMatrix" ] }, { "page": "makeInteractTrack-deprecated", "title": "*[Deprecated]* Export predicted gene-pair interaction", "topics": [ "makeInteractTrack-deprecated" ] }, { "page": "makeRiverplot-deprecated", "title": "*[Deprecated]* Generate a river (Sankey) plot", "topics": [ "makeRiverplot-deprecated" ] }, { "page": "mapCellMeta", "title": "Create new variable from categories in cellMeta", "topics": [ "mapCellMeta" ] }, { "page": "mergeH5", "title": "Merge hdf5 files", "topics": [ "mergeH5" ] }, { "page": "mergeSparseAll", "title": "Merge matrices while keeping the union of rows", "topics": [ "mergeDenseAll", "mergeSparseAll" ] }, { "page": "modalOf", "title": "Return preset modality of a ligerDataset object or that of all datasets in a liger object", "topics": [ "modalOf" ] }, { "page": "normalize", "title": "*[Deprecated]* Normalize raw counts data", "topics": [ "normalize", "normalize.DelayedArray", "normalize.dgCMatrix", "normalize.liger", "normalize.ligerDataset", "normalize.matrix", "normalize.Seurat", "normalizePeak" ] }, { "page": "online_iNMF-deprecated", "title": "*[Deprecated]* Perform online iNMF on scaled datasets", "topics": [ "online_iNMF-deprecated" ] }, { "page": "optimizeALS-deprecated", "title": "*[Deprecated]* Perform iNMF on scaled datasets", "topics": [ "optimizeALS-deprecated" ] }, { "page": "optimizeNewData", "title": "Perform factorization for new data", "topics": [ "optimizeNewData" ] }, { "page": "optimizeNewK", "title": "Perform factorization for new value of k", "topics": [ "optimizeNewK" ] }, { "page": "optimizeNewLambda", "title": "Perform factorization for new lambda value", "topics": [ "optimizeNewLambda" ] }, { "page": "optimizeSubset", "title": "Perform factorization for subset of data", "topics": [ "optimizeSubset" ] }, { "page": "pbmc", "title": "liger object of PBMC subsample data with Control and Stimulated datasets", "topics": [ "pbmc" ] }, { "page": "pbmcPlot", "title": "liger object of PBMC subsample data with plotting information available", "topics": [ "pbmcPlot" ] }, { "page": "plot.factorGSEA", "title": "GSEA plot for specific gene set and factor using factorGSEA results", "topics": [ "plot.factorGSEA" ] }, { "page": "plotBarcodeRank", "title": "Create barcode-rank plot for each dataset", "topics": [ "plotBarcodeRank" ] }, { "page": "plotCellViolin", "title": "Generate violin/box plot(s) using liger object", "topics": [ "plotCellViolin" ] }, { "page": "plotClusterFactorDot", "title": "Make dot plot of factor loading in cell groups", "topics": [ "plotClusterFactorDot" ] }, { "page": "plotClusterGeneDot", "title": "Make dot plot of gene expression in cell groups", "topics": [ "plotClusterGeneDot" ] }, { "page": "plotClusterGeneViolin", "title": "Create violin plot for multiple genes grouped by clusters", "topics": [ "plotClusterGeneViolin" ] }, { "page": "plotDensityDimRed", "title": "Create density plot basing on specified coordinates", "topics": [ "plotDensityDimRed" ] }, { "page": "plotDimRed", "title": "Generate scatter plot(s) using liger object", "topics": [ "plotByDatasetAndCluster", "plotClusterDimRed", "plotDatasetDimRed", "plotDimRed", "plotFactorDimRed", "plotGeneDimRed", "plotPeakDimRed" ] }, { "page": "plotEnhancedVolcano", "title": "Create volcano plot with EnhancedVolcano", "topics": [ "plotEnhancedVolcano" ] }, { "page": "plotHeatmap", "title": "Plot Heatmap of Gene Expression or Factor Loading", "topics": [ "plotFactorHeatmap", "plotGeneHeatmap" ] }, { "page": "plotGeneLoadings", "title": "Visualize factor expression and gene loading", "topics": [ "plotGeneLoadingRank", "plotGeneLoadings" ] }, { "page": "plotViolin", "title": "Visualize gene expression or cell metadata with violin plot", "topics": [ "plotGeneDetectedViolin", "plotGeneViolin", "plotTotalCountViolin" ] }, { "page": "plotGODot", "title": "Visualize GO enrichment test result in dot plot", "topics": [ "plotGODot" ] }, { "page": "plotGroupClusterDimRed", "title": "Comprehensive group splited cluster plot on dimension reduction with proportion", "topics": [ "plotGroupClusterDimRed" ] }, { "page": "plotMarkerHeatmap", "title": "Create heatmap for showing top marker expression in conditions", "topics": [ "plotMarkerHeatmap" ] }, { "page": "plotPairwiseDEGHeatmap", "title": "Create heatmap for pairwise DEG analysis result", "topics": [ "plotPairwiseDEGHeatmap" ] }, { "page": "plotProportion", "title": "Visualize proportion across two categorical variables", "topics": [ "plotClusterProportions", "plotProportion", "plotProportionBar", "plotProportionDot", "plotProportionPie" ] }, { "page": "plotProportionBox", "title": "Box plot of cluster proportion in each dataset, grouped by condition", "topics": [ "plotProportionBox" ] }, { "page": "plotSankey", "title": "Make Riverplot/Sankey diagram that shows label mapping across datasets", "topics": [ "plotSankey" ] }, { "page": "plotSpatial", "title": "Visualize a spatial dataset", "topics": [ "plotSpatial2D", "plotSpatial2D.liger", "plotSpatial2D.ligerSpatialDataset" ] }, { "page": "plotVarFeatures", "title": "Plot the variance vs mean of feature expression", "topics": [ "plotVarFeatures" ] }, { "page": "plotVolcano", "title": "Create volcano plot for Wilcoxon test result", "topics": [ "plotVolcano" ] }, { "page": "print.factorGSEA", "title": "Show information about factorGSEA object", "topics": [ "print.factorGSEA" ] }, { "page": "quantile_norm-deprecated", "title": "*[Superseded]* Quantile align (normalize) factor loading", "topics": [ "quantile_norm-deprecated" ] }, { "page": "quantileAlignSNF", "title": "*[Superseded]* Quantile align (normalize) factor loadings", "topics": [ "quantileAlignSNF" ] }, { "page": "quantileNorm", "title": "Quantile Align (Normalize) Factor Loadings", "topics": [ "quantileNorm", "quantileNorm.liger", "quantileNorm.Seurat" ] }, { "page": "peak", "title": "Access ligerATACDataset peak data", "topics": [ "normPeak", "normPeak,liger,character-method", "normPeak,ligerATACDataset,missing-method", "normPeak<-", "normPeak<-,liger,character-method", "normPeak<-,ligerATACDataset,missing-method", "rawPeak", "rawPeak,liger,character-method", "rawPeak,ligerATACDataset,missing-method", "rawPeak<-", "rawPeak<-,liger,character-method", "rawPeak<-,ligerATACDataset,missing-method" ] }, { "page": "read10X", "title": "Load in data from 10X", "topics": [ "read10X", "read10XATAC", "read10XRNA" ] }, { "page": "read10XFiles", "title": "Read 10X cellranger files (matrix, barcodes and features) into R session", "topics": [ "read10XFiles" ] }, { "page": "read10XH5", "title": "Read 10X HDF5 file", "topics": [ "read10XH5", "read10XH5Delay", "read10XH5Mem" ] }, { "page": "readH5AD", "title": "Read matrix from H5AD file", "topics": [ "readH5AD", "readH5ADDelay", "readH5ADMem" ] }, { "page": "readLiger", "title": "Read liger object from RDS file", "topics": [ "readLiger" ] }, { "page": "readSubset", "title": "*[Superseded]* See 'downsample'", "topics": [ "readSubset" ] }, { "page": "removeMissing", "title": "Remove missing cells or features from liger object", "topics": [ "removeMissing", "removeMissingObs" ] }, { "page": "restoreH5Liger", "title": "Restore links (to HDF5 files) for reloaded liger/ligerDataset object", "topics": [ "restoreH5Liger", "restoreOnlineLiger" ] }, { "page": "retrieveCellFeature", "title": "Retrieve a single matrix of cells from a slot", "topics": [ "retrieveCellFeature" ] }, { "page": "reverseMethData", "title": "Create \"scaled data\" for DNA methylation datasets", "topics": [ "reverseMethData" ] }, { "page": "runCINMF", "title": "Perform consensus iNMF on scaled datasets", "topics": [ "runCINMF", "runCINMF.liger", "runCINMF.Seurat" ] }, { "page": "runCluster", "title": "SNN Graph Based Community Detection", "topics": [ "runCluster" ] }, { "page": "runGeneralQC", "title": "General QC for liger object", "topics": [ "runGeneralQC" ] }, { "page": "runGOEnrich", "title": "Run Gene Ontology enrichment analysis on differentially expressed genes.", "topics": [ "runGOEnrich" ] }, { "page": "runGSEA", "title": "Analyze biological interpretations of metagene", "topics": [ "runGSEA" ] }, { "page": "runINMF", "title": "Perform iNMF on scaled datasets", "topics": [ "runINMF", "runINMF.liger", "runINMF.Seurat" ] }, { "page": "runIntegration", "title": "Integrate scaled datasets with iNMF or variant methods", "topics": [ "runIntegration", "runIntegration.liger", "runIntegration.Seurat" ] }, { "page": "runOnlineINMF", "title": "Perform online iNMF on scaled datasets", "topics": [ "runOnlineINMF", 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