Man pages for quadbiolab/Pando
Inferring regulomes from multi-modal single-cell genomics data
| aggregate_assay | Aggregate Seurat assay over groups |
| aggregate_matrix | Aggregate matrix over groups |
| coef | Get fitted coefficients |
| create_GRNData | Create GRNData object from a Seurat and a GRN object |
| DefaultNetwork | Get active network |
| dMcast | Copy of the dMcast function from the Matrix.utils package,... |
| fast_aggregate | Copy of the aggregate.Matrix function from the Matrix.utils... |
| find_modules | Find TF modules in regulatory network |
| find_motifs | Scan for motifs in candidate regions. |
| find_peaks_near_genes | Find peaks or regions near gene body or TSS |
| fit_bagging_ridge | Fit a bagging ridge regression model as implemented in... |
| fit_bayesian_ridge | Fit a bayesian ridge regression model as implemented in... |
| fit_brms | Fit a Bayesian regression model with brms and Stan |
| fit_cvglmnet | Cross-validation for regularized generalized linear models |
| fit_glm | Fit generalized linear model |
| fit_glmnet | Fit regularized generalized linear model |
| fit_grn_models | Fit models for gene expression |
| fit_model | Fit (regularized) generalized linear model |
| fit_xgb | Fit a gradient boosting regression model with XGBoost |
| format_coefs | Format network coefficients |
| GetAssay | Get Seurat assay from GRNData |
| GetAssaySummary | Get summary of seurat assay |
| GetGRN | Get network data |
| GetNetwork | Get network |
| get_network_graph | Compute network graph embedding using UMAP. |
| get_tf_network | Get sub-network centered around one TF. |
| get_umap | Compute UMAP embedding |
| gof | Get goodness-of-fit info |
| GRNData-class | The GRNData class |
| hello | Hello, World! |
| infer_grn | Infer a Gene Regulatory Network with 'Pando' |
| initiate_grn | Initiate the 'RegulatoryNetwork' object. |
| LayerData | Get layer data from GRNData |
| log_message | Print diagnostic message |
| map_par | Apply function over a List or Vector (in parallel) |
| Network-class | The Modules class |
| NetworkFeatures | Get network features |
| NetworkGraph | Get network parameters |
| NetworkModules | Get TF modules |
| NetworkParams | Get network parameters |
| NetworkRegions | Get network regions |
| NetworkTFs | Get network TFs |
| no_legend | Removes legend from plot. |
| no_margin | Removes margins from plot. |
| no_x_text | Removes x axis text. |
| no_y_text | Removes y axis text. |
| Params | Get GRN inference parameters |
| plot_gof | Plot goodness-of-fit metrics. |
| plot_module_metrics | Plot module metrics number of genes, number of peaks and... |
| plot_network_graph | Plot network graph. |
| plot_tf_network | Plot sub-network centered around one TF. |
| Print RegulatoryNetwork objects | |
| r2 | R^2 (coefficient of determination) |
| Regions-class | The Regions class |
| RegulatoryNetwork-class | The RegularotyNetwork class |
| rse | Relative Squared Error |
| sparse_cor | Safe correlation function which returns a sparse matrix... |
| sparse_covcor | Fast correlation and covariance calcualtion for sparse... |
| sse | Sum of Squared Errors |
| VariableFeatures | Get variable features from GRNData |
