Man pages for tinglab/redPATH
Reconstructing the pseudo development time of cell lineages in single cell RNA-Seq data and applications in cancer.
| bubblesort_index | Bubblesort Index |
| calc_all_hmm_diff_parallel | HMM segmentation for each gene |
| calc_correlation | Calculate correlation of gene expression with pseudotime |
| change_index | Change Index |
| distribution_plot | Visualization of G0-like distribution in mean scores |
| ensembl_to_mgi | Gene name conversion: ENSEMBL -> MGI |
| entrez_to_mgi | Gene name conversion: ENTREZ -> MGI |
| filter_exp | Filter genes |
| gene_selection | Selects significant genes |
| gene_selection_intersection | Selects significant genes |
| get_gene_cluster | Gene Clustering |
| get_GO_exp | Preprocess Gene Expression |
| get_specific_gene_exprs | Search for specific gene expression |
| hamiltonian_path_as | Hamiltonian Path - Modified Arbitrary Insertion |
| hamiltonian_path_force | Hamiltonian path - by brute force |
| infer_GO_summaries | Infer Gene Ontology summaries |
| kendall_correlation | Kendall Correlation |
| kl_cpp | Fast implementation of KL distance |
| kmeans_clustering | Kmeans Clustering - returns classification result |
| llorens_exprs | Llorens-B - single cell neural stem cells dataset. |
| llorens_labels | Llorens-B - single cell neural stem cells dataset. |
| mean_score_plot | Visualization of G0-like distribution in mean scores along a... |
| mgh107_portal_exprs | MGH107 - single cell glioma dataset of MGH107 patient. |
| mgh107_portal_labels | MGH107 - single cell glioma dataset of MGH107 patient. |
| mgi_to_entrez | Gene name conversion: MGI -> ENTREZ |
| plot_cycle_diff_3d | Coupling cell cycle and differentiation 3-D plots |
| plot_diff_3d | Coupling cell cycle and differentiation 3-D plots - Gene... |
| plot_gene_exprs | Plot function for specific gene expression changes |
| plot_heatmap_analysis | Heatmap Analysis |
| plot_hmm_full | Plot function for HMM & gene expression changes |
| plot_specific_gene_exprs | Plot function for specific gene expression changes |
| redpath | redPATH Pseudotime |
| statistical_test | Identification of G0-like cells |
