Man pages for CHuanSite/SJD
Structured Joint Decomposition (SJD)
| addSJDtoSeurat | Add SJD loadings to a Seurat object |
| assemble.byComponent | Assemble Files Based on Component |
| assemble.byDataset | Assemble files based on Dataset |
| balanceData | Balance Data |
| BEMA | BEMA for the standard spiked covariance model |
| compNameAssign | Components Name Assignment for concatenate, joint and... |
| compNameAssignSep | Components Name Assignment for Seperate Analysis |
| concatICA | Concatenated decomposition with Independent Component... |
| concatNMF | Concatenated decomposition with Nonnegative Matrix... |
| concatPCA | Concatenated Decomposition with Principal Component Analysis |
| configuration_setting_generation | Configuration for simulated data generation |
| datasetNameExtractor | Dataset Name Extractor |
| filterNAValue | Filter NA Value |
| frameToMatrix | Transform data.frame to matrix |
| geneNameAssign | Gene name assignment |
| geneNameExtractor | Gene Name Extractor |
| geneScreen | Gene Screen |
| getMatch | Species matching function |
| groupNameExtractor | Group Name Extractor |
| jointICA | Joint decomposition with Independent Component Analysis |
| jointNMF | Joint Decomposition with Nonnegative Matrix Factorization |
| jointPCA | Joint Decomposition with Principal Component Analysis |
| linkedPCA | Linked Component Analysis |
| marchenko_pastur_quantile | Quantile for Marchenko Pastur Distribution |
| min_max_normalization | Min-Max Normalization Function |
| mtx | mtx sequence data |
| NeuroGenesis4 | NeuroGenesis4 |
| NeuroGenesis4.afterWrap | NeuroGenesis4.afterWrap |
| NeuroGenesis4.info | NeuroGenesis4.info |
| newNMF | Function to estimate sample embeddings for one dataset from a... |
| normalizeData | Data Normalization |
| Procrustes | Procrustes Projection |
| projectiLCA | Function to estimate sample embeddings for one dataset from a... |
| projectNMF | Function to estimate sample embeddings for one dataset from a... |
| pveMultiple | Percentage of Variance Explained for Multiple Data sets |
| pveSep | Percentage of Variance Explained for separate data set |
| rebalanceData | Rebalance Data |
| rotate_component | Simulated Component Rotation |
| sampleNameAssign | Sample Name Assignment for Concatenate, Joint and TwoStageLCA... |
| sampleNameAssignProj | Sample Name Assignment for projectNMF |
| sampleNameAssignSep | Sample Name Assignment for Seperate Analysis |
| sampleNameExtractor | Sample name extractor |
| score_generation | Random Score Generation |
| scoreNameAssign | Score Name Assignment for Concatenate, Joint and TwoStageLCA... |
| scoreNameAssignProj | Score Name Assignment for projectNMF |
| scoreNameAssignSep | Score Name Assign for Seperate Analysis |
| ScreePlot_LCvsPC | genetrate scree plot using tsLCA and sepPCA embeddings for... |
| sepICA | Single Data Set Decomposition with Independent Component... |
| sepNMF | Single Data Set Decomposition with Nonnegative Matrix... |
| sepPCA | Single Data Set Decomposition with Principal Component... |
| simulated_data_generation | Simulated Data Generation |
| SJDScorePlotter | Plot SJD score |
| sjdWrap | SJD Wrap |
| sjdWrapProjection | SJD Wrap for projection |
| twoStageiLCA | Two-staged Independent Linked Component Analysis |
| twoStageiLCA.rank | Two-staged Independent LCA and automatic rank selection |
| twoStageLCA | Two-staged Linked Component Analysis |
| twoStageLCA.rank | Two-staged LCA and automatic rank selection |
| umap_tsne_onLC | genetrate new UMAP and TSNE coordinates given LCA object |
| weightData | Weighting Data Set |
