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| liger-package | Linked Inference of Genomic Experimental Relationships |
| %>% | Pipe operator |
| aggregateByCluster | Aggregate gene-level measurements across cells within clusters to allow correlation across datasets |
| alignment_metric_per_factor | Calculate alignment metric per factor. |
| calcAgreement | Calculate agreement metric |
| calcAlignment | Calculate alignment metric |
| calcAlignmentPerCluster | Calculate alignment for each cluster |
| calcARI | Calculate adjusted Rand index |
| calcDatasetSpecificity | Calculate a dataset-specificity score for each factor |
| calcPurity | Calculate purity |
| clusterLouvainJaccard | Perform graph-based clustering (Louvain algorithm) using number of shared nearest neighbors (Jaccard index) as a distance metric. Note that use of this function requires Seurat to be loaded. |
| convertOldLiger | Convert older liger object into most current version (based on class definition) |
| createLiger | Create a liger object. |
| getFactorMarkers | Find shared and dataset-specific markers |
| getGeneValues | Get gene expression values from list of expression matrices. |
| getProportionMito | Calculate proportion mitochondrial contribution |
| imputeKNN | Impute the query cell expression matrix |
| liger | Linked Inference of Genomic Experimental Relationships |
| liger | The LIGER Class |
| liger-class | The LIGER Class |
| ligerToSeurat | Create a Seurat object containing the data from a liger object |
| linkGenesAndPeaks | Linking genes to putative regulatory elements |
| louvainCluster | Louvain algorithm for community detection |
| makeInteractTrack | Export predicted gene-pair interaction |
| makeRiverplot | Generate a river (Sankey) plot |
| Matrix.column_norm | Perform fast and memory-efficient normalization operation on sparse matrix data. |
| nnzeroGroups | nnzeroGroups |
| nnzeroGroups.dgCMatrix | nnzeroGroups |
| nnzeroGroups.matrix | nnzeroGroups |
| normalize | Normalize raw datasets to column sums |
| optimizeALS | Perform iNMF on scaled datasets |
| optimizeALS.liger | Perform iNMF on scaled datasets |
| optimizeALS.list | 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 |
| plotByDatasetAndCluster | Plot t-SNE coordinates of cells across datasets |
| plotClusterFactors | Plot heatmap of cluster/factor correspondence |
| plotClusterProportions | Plot cluster proportions by dataset |
| plotFactors | Plot scatter plots of unaligned and aligned factor loadings |
| plotFeature | Plot specific feature on t-SNE coordinates |
| plotGene | Plot gene expression on dimensional reduction (t-SNE) coordinates |
| plotGeneLoadings | Generate t-SNE plots and gene loading plots |
| plotGenes | Plot expression of multiple genes |
| plotGeneViolin | Plot violin plots for gene expression |
| plotWordClouds | Generate word clouds and t-SNE plots |
| quantileAlignSNF | Quantile align (normalize) factor loadings |
| quantileAlignSNF.liger | Quantile align (normalize) factor loadings |
| quantileAlignSNF.list | Quantile align (normalize) factor loadings |
| quantile_norm | Quantile align (normalize) factor loadings |
| rank_matrix | rank_matrix |
| rank_matrix.dgCMatrix | rank_matrix |
| rank_matrix.matrix | rank_matrix |
| read10X | Read 10X alignment data (including V3) |
| removeMissingObs | Remove cells/genes with no expression across any genes/cells |
| reorganizeLiger | Construct a liger object organized by another feature |
| runTSNE | Perform t-SNE dimensionality reduction |
| runUMAP | Perform UMAP dimensionality reduction |
| runWilcoxon | Perform Wilcoxon rank-sum test |
| scaleNotCenter | Scale genes by root-mean-square across cells |
| scaleNotCenter_sparse | Perform fast and memory-efficient data scaling operation on sparse matrix data. |
| selectGenes | Select a subset of informative genes |
| seuratToLiger | Create liger object from one or more Seurat objects |
| show | show method for liger |
| show-method | show method for liger |
| SNF | Generate shared factor neighborhood graph |
| SNF.liger | Generate shared factor neighborhood graph |
| SNF.list | Generate shared factor neighborhood graph |
| subsetLiger | Construct a liger object with a specified subset |
| suggestK | Visually suggest appropiate k value |
| suggestLambda | Visually suggest appropriate lambda value |
| sumGroups | sumGroups |
| sumGroups.dgCMatrix | sumGroups |
| sumGroups.matrix | sumGroups |