API for rliger
Linked Inference of Genomic Experimental Relationships
| Global functions | |
|---|---|
| ComputeSNN | Source code |
| DirectSNNToFile | Source code |
| GroupSingletons | Source code |
| Matrix.column_norm | Source code |
| MergeSparseDataAll | Source code |
| RunModularityClusteringCpp | Source code |
| SLMCluster | Source code |
| WriteEdgeFile | Source code |
| addMissingCells | Source code |
| assign.singletons | Source code |
| assign.singletons.list | Source code |
| calcARI | Man page Source code |
| calcAgreement | Man page Source code |
| calcAlignment | Man page Source code |
| calcAlignmentPerCluster | Man page Source code |
| calcDatasetSpecificity | Man page Source code |
| calcGeneVars | Man page |
| calcNormLoadings | Man page Source code |
| calcPurity | Man page Source code |
| cluster_vote | Source code |
| compute_pval | Source code |
| compute_ustat | Source code |
| convertOldLiger | Man page Source code |
| cpp_in_place_rank_mean | Source code |
| cpp_nnzeroGroups_dense | Source code |
| cpp_nnzeroGroups_dense_T | Source code |
| cpp_nnzeroGroups_dgc | Source code |
| cpp_nnzeroGroups_dgc_T | Source code |
| cpp_rank_matrix_dense | Source code |
| cpp_rank_matrix_dgc | Source code |
| cpp_sumGroups_dense | Source code |
| cpp_sumGroups_dense_T | Source code |
| cpp_sumGroups_dgc | Source code |
| cpp_sumGroups_dgc_T | Source code |
| createLiger | Man page Source code |
| ctrl | Man page |
| downsample | Source code |
| fftRtsne | Source code |
| fplot | Source code |
| frobenius_prod | Source code |
| getFactorMarkers | Man page Source code |
| getGeneValues | Man page Source code |
| getMode | Source code |
| getProportionMito | Man page Source code |
| imputeKNN | Man page Source code |
| kl_divergence_uniform | Source code |
| liger | Man page |
| liger-class | Man page |
| ligerToSeurat | Man page Source code |
| linkGenesAndPeaks | Man page Source code |
| louvainCluster | Man page Source code |
| makeFeatureMatrix | Man page Source code |
| makeInteractTrack | Man page Source code |
| makeRiverplot | Man page Source code |
| max_factor | Source code |
| mergeH5 | Man page Source code |
| nmf_hals | Source code |
| nnzeroGroups | Source code |
| nnzeroGroups.dgCMatrix | Source code |
| nnzeroGroups.matrix | Source code |
| nonneg | Source code Source code |
| normalize | Man page Source code |
| online_iNMF | Man page Source code |
| optimizeALS | Man page Source code |
| optimizeALS.liger | Man page Source code |
| optimizeALS.list | Man page Source code |
| optimizeNewData | Man page Source code |
| optimizeNewK | Man page Source code |
| optimizeNewLambda | Man page Source code |
| optimizeSubset | Man page Source code |
| optimize_UANLS | Source code |
| plotByDatasetAndCluster | Man page Source code |
| plotClusterFactors | Man page Source code |
| plotClusterProportions | Man page Source code |
| plotFactors | Man page Source code |
| plotFeature | Man page Source code |
| plotGene | Man page Source code |
| plotGeneLoadings | Man page Source code |
| plotGeneViolin | Man page Source code |
| plotGenes | Man page Source code |
| plotWordClouds | Man page Source code |
| quantileAlignSNF | Man page Source code |
| quantile_norm | Man page Source code |
| quantile_norm.liger | Man page Source code |
| quantile_norm.list | Man page Source code |
| rank_matrix | Source code |
| rank_matrix.dgCMatrix | Source code |
| rank_matrix.matrix | Source code |
| rbindlist | Source code |
| read10X | Man page Source code |
| readSubset | Man page Source code |
| refine_clusts_knn | Source code |
| removeMissingObs | Man page Source code |
| reorganizeLiger | Man page Source code |
| restoreOnlineLiger | Man page Source code |
| rowMeansFast | Source code |
| rowVarsFast | Source code |
| runGSEA | Man page Source code |
| runTSNE | Man page Source code |
| runUMAP | Man page Source code |
| runWilcoxon | Man page Source code |
| safe_h5_create | Source code |
| scaleL2norm | Source code |
| scaleNotCenter | Man page Source code |
| scaleNotCenterFast | Source code |
| scale_columns_fast | Source code |
| selectGenes | Man page Source code |
| seuratToLiger | Man page Source code |
| show | Man page |
| show,liger-method | Man page |
| solveNNLS | Source code |
| sparse.transpose | Source code |
| sparse.var | Source code |
| stim | Man page |
| subsetLiger | Man page Source code |
| suggestK | Man page Source code |
| suggestLambda | Man page Source code |
| sumGroups | Source code |
| sumGroups.dgCMatrix | Source code |
| sumGroups.matrix | Source code |
| sumSquaredDeviations | Source code |
| tidy_results | Source code |
| wilcoxauc | Source code |
