A B C D E F G H I L M N O P Q R S U V W misc
| alignFactors | Align factor loadings to get final integration |
| alignFactors.liger | Align factor loadings to get final integration |
| alignFactors.Seurat | Align factor loadings to get final integration |
| as.liger | Converting other classes of data to a liger object |
| as.liger.dgCMatrix | Converting other classes of data to a liger object |
| as.liger.Seurat | Converting other classes of data to a liger object |
| as.liger.SingleCellExperiment | Converting other classes of data to a liger object |
| as.ligerDataset | Converting other classes of data to a ligerDataset object |
| as.ligerDataset.default | Converting other classes of data to a ligerDataset object |
| as.ligerDataset.ligerDataset | Converting other classes of data to a ligerDataset object |
| as.ligerDataset.matrix | Converting other classes of data to a ligerDataset object |
| as.ligerDataset.Seurat | Converting other classes of data to a ligerDataset object |
| as.ligerDataset.SingleCellExperiment | Converting other classes of data to a ligerDataset object |
| bmmc | liger object of bone marrow subsample data with RNA and ATAC modality |
| c.liger | liger class |
| calcAgreement | Calculate agreement metric after integration |
| calcAlignment | Calculate alignment metric after integration |
| calcARI | Calculate adjusted Rand index (ARI) by comparing two cluster labeling variables |
| calcDatasetSpecificity | Calculate a dataset-specificity score for each factor |
| calcNMI | Calculate Normalized Mutual Information (NMI) by comparing two cluster labeling variables |
| calcPurity | Calculate purity by comparing two cluster labeling variables |
| cbind.ligerDataset | ligerDataset class |
| cellMeta | liger class |
| cellMeta-method | liger class |
| cellMeta<- | liger class |
| cellMeta<--method | liger class |
| centroidAlign | *[Experimental]* Align factor loading by centroid alignment (beta) |
| centroidAlign.liger | *[Experimental]* Align factor loading by centroid alignment (beta) |
| centroidAlign.Seurat | *[Experimental]* Align factor loading by centroid alignment (beta) |
| closeAllH5 | Close all links (to HDF5 files) of a liger object |
| closeAllH5.liger | Close all links (to HDF5 files) of a liger object |
| closeAllH5.ligerDataset | Close all links (to HDF5 files) of a liger object |
| commandDiff | Check difference of two liger command |
| commands | liger class |
| commands-method | liger class |
| convertOldLiger | Convert old liger object to latest version |
| coordinate | Access ligerSpatialDataset coordinate data |
| coordinate-method | Access ligerSpatialDataset coordinate data |
| coordinate<- | Access ligerSpatialDataset coordinate data |
| coordinate<--method | Access ligerSpatialDataset coordinate data |
| createH5LigerDataset | Create on-disk ligerDataset Object |
| createLiger | Create liger object |
| createLigerDataset | Create in-memory ligerDataset object |
| dataset | liger class |
| dataset-method | liger class |
| dataset<- | liger class |
| dataset<--method | liger class |
| datasets | liger class |
| datasets-method | liger class |
| datasets<- | liger class |
| datasets<--method | liger class |
| defaultCluster | liger class |
| defaultCluster-method | liger class |
| defaultCluster<- | liger class |
| defaultCluster<--method | liger class |
| defaultDimRed | liger class |
| defaultDimRed-method | liger class |
| defaultDimRed<- | liger class |
| defaultDimRed<--method | liger class |
| deg.marker | Data frame for example marker DEG test result |
| deg.pw | Data frame for example pairwise DEG test result |
| dim-method | liger class |
| dim-method | ligerDataset class |
| dimnames-method | liger class |
| dimnames-method | ligerDataset class |
| dimnames<--method | liger class |
| dimnames<--method | ligerDataset class |
| dimRed | liger class |
| dimRed-method | liger class |
| dimRed<- | liger class |
| dimRed<--method | liger class |
| dimReds | liger class |
| dimReds-method | liger class |
| dimReds<- | liger class |
| dimReds<--method | liger class |
| downsample | Downsample datasets |
| exportInteractTrack | Export predicted gene-pair interaction |
| featureMeta | ligerDataset class |
| featureMeta-method | ligerDataset class |
| featureMeta<- | ligerDataset class |
| featureMeta<--method | ligerDataset class |
| fortify.liger | liger class |
| getFactorMarkers | Find shared and dataset-specific markers |
| getH5File | ligerDataset class |
| getH5File-method | liger class |
| getH5File-method | ligerDataset class |
| getMatrix | ligerDataset class |
| getMatrix-method | liger class |
| getMatrix-method | ligerDataset class |
| getProportionMito | Calculate proportion mitochondrial contribution |
| H5Apply | Apply function to chunks of H5 data in ligerDataset object |
| h5fileInfo | ligerDataset class |
| h5fileInfo-method | ligerDataset class |
| h5fileInfo<- | ligerDataset class |
| h5fileInfo<--method | ligerDataset class |
| importBMMC | Import prepared dataset publically available |
| importCGE | Import prepared dataset publically available |
| importPBMC | Import prepared dataset publically available |
| imputeKNN | Impute the peak counts from gene expression data referring to an ATAC dataset after integration |
| is.newLiger | Check if given liger object if under new implementation |
| isH5Liger | Check if a liger or ligerDataset object is made of HDF5 file |
| length.liger | liger class |
| lengths.liger | liger class |
| liger | liger class |
| liger-class | liger class |
| ligerATACDataset | Subclass of ligerDataset for ATAC modality |
| ligerATACDataset-class | Subclass of ligerDataset for ATAC modality |
| ligerCommand | ligerCommand object: Record the input and time of a LIGER function call |
| ligerCommand-class | ligerCommand object: Record the input and time of a LIGER function call |
| ligerDataset | ligerDataset class |
| ligerDataset-class | ligerDataset class |
| ligerMethDataset | Subclass of ligerDataset for Methylation modality |
| ligerMethDataset-class | Subclass of ligerDataset for Methylation modality |
| ligerRNADataset | Subclass of ligerDataset for RNA modality |
| ligerRNADataset-class | Subclass of ligerDataset for RNA modality |
| ligerSpatialDataset | Subclass of ligerDataset for Spatial modality |
| ligerSpatialDataset-class | Subclass of ligerDataset for Spatial modality |
| ligerToSeurat | Convert between liger and Seurat object |
| linkGenesAndPeaks | Linking genes to putative regulatory elements |
| louvainCluster-deprecated | *[Superseded]* Louvain algorithm for community detection |
| makeFeatureMatrix | Fast calculation of feature count matrix |
| makeInteractTrack-deprecated | *[Deprecated]* Export predicted gene-pair interaction |
| makeRiverplot-deprecated | *[Deprecated]* Generate a river (Sankey) plot |
| mapCellMeta | Create new variable from categories in cellMeta |
| mergeDenseAll | Merge matrices while keeping the union of rows |
| mergeH5 | Merge hdf5 files |
| mergeSparseAll | Merge matrices while keeping the union of rows |
| modalOf | Return preset modality of a ligerDataset object or that of all datasets in a liger object |
| names.liger | liger class |
| names<-.liger | liger class |
| normalize | *[Deprecated]* Normalize raw counts data |
| normalize.DelayedArray | *[Deprecated]* Normalize raw counts data |
| normalize.dgCMatrix | *[Deprecated]* Normalize raw counts data |
| normalize.liger | *[Deprecated]* Normalize raw counts data |
| normalize.ligerDataset | *[Deprecated]* Normalize raw counts data |
| normalize.matrix | *[Deprecated]* Normalize raw counts data |
| normalize.Seurat | *[Deprecated]* Normalize raw counts data |
| normalizePeak | *[Deprecated]* Normalize raw counts data |
| normData | ligerDataset class |
| normData-method | liger class |
| normData-method | ligerDataset class |
| normData<- | ligerDataset class |
| normData<--method | liger class |
| normData<--method | ligerDataset class |
| normPeak | Access ligerATACDataset peak data |
| normPeak-method | Access ligerATACDataset peak data |
| normPeak<- | Access ligerATACDataset peak data |
| normPeak<--method | Access ligerATACDataset peak data |
| online_iNMF-deprecated | *[Deprecated]* Perform online iNMF on scaled datasets |
| optimizeALS-deprecated | *[Deprecated]* Perform iNMF on scaled datasets |
| optimizeNewData | Perform factorization for new data |
| optimizeNewK | Perform factorization for new value of k |
| optimizeNewLambda | Perform factorization for new lambda value |
| optimizeSubset | Perform factorization for subset of data |
| pbmc | liger object of PBMC subsample data with Control and Stimulated datasets |
| pbmcPlot | liger object of PBMC subsample data with plotting information available |
| plotBarcodeRank | Create barcode-rank plot for each dataset |
| plotByDatasetAndCluster | Generate scatter plot(s) using liger object |
| plotCellViolin | Generate violin/box plot(s) using liger object |
| plotClusterDimRed | Generate scatter plot(s) using liger object |
| plotClusterFactorDot | Make dot plot of factor loading in cell groups |
| plotClusterGeneDot | Make dot plot of gene expression in cell groups |
| plotClusterGeneViolin | Create violin plot for multiple genes grouped by clusters |
| plotClusterProportions | Visualize proportion across two categorical variables |
| plotDatasetDimRed | Generate scatter plot(s) using liger object |
| plotDensityDimRed | Create density plot basing on specified coordinates |
| plotDimRed | Generate scatter plot(s) using liger object |
| plotEnhancedVolcano | Create volcano plot with EnhancedVolcano |
| plotFactorDimRed | Generate scatter plot(s) using liger object |
| plotFactorHeatmap | Plot Heatmap of Gene Expression or Factor Loading |
| plotGeneDetectedViolin | Visualize gene expression or cell metadata with violin plot |
| plotGeneDimRed | Generate scatter plot(s) using liger object |
| plotGeneHeatmap | Plot Heatmap of Gene Expression or Factor Loading |
| plotGeneLoadingRank | Visualize factor expression and gene loading |
| plotGeneLoadings | Visualize factor expression and gene loading |
| plotGeneViolin | Visualize gene expression or cell metadata with violin plot |
| plotGODot | Visualize GO enrichment test result in dot plot |
| plotGroupClusterDimRed | Comprehensive group splited cluster plot on dimension reduction with proportion |
| plotMarkerHeatmap | Create heatmap for showing top marker expression in conditions |
| plotPairwiseDEGHeatmap | Create heatmap for pairwise DEG analysis result |
| plotPeakDimRed | Generate scatter plot(s) using liger object |
| plotProportion | Visualize proportion across two categorical variables |
| plotProportionBar | Visualize proportion across two categorical variables |
| plotProportionBox | Box plot of cluster proportion in each dataset, grouped by condition |
| plotProportionDot | Visualize proportion across two categorical variables |
| plotProportionPie | Visualize proportion across two categorical variables |
| plotSankey | Make Riverplot/Sankey diagram that shows label mapping across datasets |
| plotSpatial2D | Visualize a spatial dataset |
| plotSpatial2D.liger | Visualize a spatial dataset |
| plotSpatial2D.ligerSpatialDataset | Visualize a spatial dataset |
| plotTotalCountViolin | Visualize gene expression or cell metadata with violin plot |
| plotVarFeatures | Plot the variance vs mean of feature expression |
| plotVolcano | Create volcano plot for Wilcoxon test result |
| quantileAlignSNF | *[Superseded]* Quantile align (normalize) factor loadings |
| quantileNorm | Quantile Align (Normalize) Factor Loadings |
| quantileNorm.liger | Quantile Align (Normalize) Factor Loadings |
| quantileNorm.Seurat | Quantile Align (Normalize) Factor Loadings |
| quantile_norm-deprecated | *[Superseded]* Quantile align (normalize) factor loading |
| rawData | ligerDataset class |
| rawData-method | liger class |
| rawData-method | ligerDataset class |
| rawData<- | ligerDataset class |
| rawData<--method | liger class |
| rawData<--method | ligerDataset class |
| rawPeak | Access ligerATACDataset peak data |
| rawPeak-method | Access ligerATACDataset peak data |
| rawPeak<- | Access ligerATACDataset peak data |
| rawPeak<--method | Access ligerATACDataset peak data |
| read10X | Load in data from 10X |
| read10XATAC | Load in data from 10X |
| read10XFiles | Read 10X cellranger files (matrix, barcodes and features) into R session |
| read10XH5 | Read 10X HDF5 file |
| read10XH5Delay | Read 10X HDF5 file |
| read10XH5Mem | Read 10X HDF5 file |
| read10XRNA | Load in data from 10X |
| readH5AD | Read matrix from H5AD file |
| readH5ADDelay | Read matrix from H5AD file |
| readH5ADMem | Read matrix from H5AD file |
| readLiger | Read liger object from RDS file |
| readSubset | *[Superseded]* See 'downsample' |
| removeMissing | Remove missing cells or features from liger object |
| removeMissingObs | Remove missing cells or features from liger object |
| restoreH5Liger | Restore links (to HDF5 files) for reloaded liger/ligerDataset object |
| restoreOnlineLiger | Restore links (to HDF5 files) for reloaded liger/ligerDataset object |
| retrieveCellFeature | Retrieve a single matrix of cells from a slot |
| reverseMethData | Create "scaled data" for DNA methylation datasets |
| runCINMF | Perform consensus iNMF on scaled datasets |
| runCINMF.liger | Perform consensus iNMF on scaled datasets |
| runCINMF.Seurat | Perform consensus iNMF on scaled datasets |
| runCluster | SNN Graph Based Community Detection |
| runGeneralQC | General QC for liger object |
| runGOEnrich | Run Gene Ontology enrichment analysis on differentially expressed genes. |
| runGSEA | Analyze biological interpretations of metagene |
| runINMF | Perform iNMF on scaled datasets |
| runINMF.liger | Perform iNMF on scaled datasets |
| runINMF.Seurat | Perform iNMF on scaled datasets |
| runIntegration | Integrate scaled datasets with iNMF or variant methods |
| runIntegration.liger | Integrate scaled datasets with iNMF or variant methods |
| runIntegration.Seurat | Integrate scaled datasets with iNMF or variant methods |
| runMarkerDEG | Find DEG between groups |
| runOnlineINMF | Perform online iNMF on scaled datasets |
| runOnlineINMF.liger | Perform online iNMF on scaled datasets |
| runOnlineINMF.Seurat | Perform online iNMF on scaled datasets |
| runPairwiseDEG | Find DEG between groups |
| runTSNE | Perform t-SNE dimensionality reduction |
| runUINMF | Perform Mosaic iNMF (UINMF) on scaled datasets with unshared features |
| runUINMF.liger | Perform Mosaic iNMF (UINMF) on scaled datasets with unshared features |
| runUMAP | Perform UMAP Dimensionality Reduction |
| runWilcoxon | Find DEG between groups |
| scaleData | ligerDataset class |
| scaleData-method | liger class |
| scaleData-method | ligerDataset class |
| scaleData<- | ligerDataset class |
| scaleData<--method | liger class |
| scaleData<--method | ligerDataset class |
| scaleNotCenter | Scale genes by root-mean-square across cells |
| scaleNotCenter.DelayedArray | Scale genes by root-mean-square across cells |
| scaleNotCenter.dgCMatrix | Scale genes by root-mean-square across cells |
| scaleNotCenter.liger | Scale genes by root-mean-square across cells |
| scaleNotCenter.ligerDataset | Scale genes by root-mean-square across cells |
| scaleNotCenter.ligerMethDataset | Scale genes by root-mean-square across cells |
| scaleNotCenter.Seurat | Scale genes by root-mean-square across cells |
| scaleUnsharedData | ligerDataset class |
| scaleUnsharedData-method | liger class |
| scaleUnsharedData-method | ligerDataset class |
| scaleUnsharedData<- | ligerDataset class |
| scaleUnsharedData<--method | liger class |
| scaleUnsharedData<--method | ligerDataset class |
| selectBatchHVG | *[Experimental]* Batch-aware highly variable gene selection |
| selectBatchHVG.DelayedArray | *[Experimental]* Batch-aware highly variable gene selection |
| selectBatchHVG.dgCMatrix | *[Experimental]* Batch-aware highly variable gene selection |
| selectBatchHVG.liger | *[Experimental]* Batch-aware highly variable gene selection |
| selectBatchHVG.ligerDataset | *[Experimental]* Batch-aware highly variable gene selection |
| selectGenes | Select a subset of informative genes |
| selectGenes.liger | Select a subset of informative genes |
| selectGenes.Seurat | Select a subset of informative genes |
| selectGenesVST | Select variable genes from one dataset with Seurat VST method |
| seuratToLiger | Converting other classes of data to a liger object |
| show-method | liger class |
| show-method | ligerCommand object: Record the input and time of a LIGER function call |
| show-method | ligerDataset class |
| sub-liger | Subset liger with brackets |
| sub-ligerDataset | Subset ligerDataset object |
| sub-sub-liger | Get cell metadata variable |
| subsetH5LigerDataset | Subset ligerDataset object |
| subsetLiger | Subset liger object |
| subsetLigerDataset | Subset ligerDataset object |
| subsetMemLigerDataset | Subset ligerDataset object |
| suggestK | *[Experimental]* Suggest optimal K value for the factorization |
| updateLigerObject | Update old liger object to up-to-date structure |
| varFeatures | liger class |
| varFeatures-method | liger class |
| varFeatures<- | liger class |
| varFeatures<--method | liger class |
| varUnsharedFeatures | liger class |
| varUnsharedFeatures-method | liger class |
| varUnsharedFeatures<- | liger class |
| varUnsharedFeatures<--method | liger class |
| writeH5 | Write in-memory data into H5 file |
| writeH5.default | Write in-memory data into H5 file |
| writeH5.dgCMatrix | Write in-memory data into H5 file |
| writeH5.liger | Write in-memory data into H5 file |
| writeH5.ligerDataset | Write in-memory data into H5 file |
| writeH5AD | Write liger object to H5AD files |
| writeH5AD.dgCMatrix | Write liger object to H5AD files |
| writeH5AD.liger | Write liger object to H5AD files |
| writeH5AD.ligerDataset | Write liger object to H5AD files |
| $.liger | liger class |
| $<-.liger | liger class |
| .complexHeatmapDotPlot | Generate dot plot from input matrix with ComplexHeatmap |
| .ggCellViolin | Produce single violin plot with data frame passed from upstream |
| .ggplotLigerTheme | Generic ggplot theme setting for rliger package |
| .ggScatter | Produce single scatter plot with data frame passed from upstream |
| .plotHeatmap | General heatmap plotting with prepared matrix and data.frames |
| [.liger | Subset liger with brackets |
| [.ligerDataset | Subset ligerDataset object |
| [[.liger | Get cell metadata variable |
| [[<-.liger | liger class |