Man pages for juliendelile/Antler
ANother Transcriptome Lineage ExploreR
| add_color_map | Add a new color map. |
| Antler-class | Interface of the Antler package (reference class). |
| brew_more_colors | Build and name color palette vectors |
| build_pseudotime_tree | Reconstruct pseudotime tree |
| carve | Reconstruct cell state lineage trajectories |
| cell_clusters_identify | Cluster cells from a selected gene module list. |
| cell_names | Returns the current cell names. |
| cell_state_graph_plot | Plot cell state graph |
| convert_ensembl_id_to_name | Replace ensembl gene ids with gene names |
| define_cell_samples | Define the cells sample names and map the cell colors to some... |
| dispersed_genes | Print highly-dispersed genes. |
| exclude_exotic_genes | Exclude genes from their name pattern. |
| exclude_unexpressed_genes | Exclude genes with low expression. |
| export_expressionset | Export internal expression set. |
| gene_modules_export | Save gene module to file. |
| gene_modules_identify | Identify gene modules. |
| gene_modules_report_genes | Report whether genes belong to modules |
| gene_modules_select_from_gene_names | Select gene modules from gene names |
| gene_modules_select_from_ids | Select gene modules from indices |
| gene_names | Returns the current gene names. |
| genes_from_GOterms | Convert GO terms to gene names. |
| load_dataset | Import a RNA-seq dataset into Antler. |
| normalize | Normalize gene expression levels. |
| num_cells | Returns the current number of cells. |
| num_genes | Returns the current number of genes. |
| plot_pseudotime_dynamics | Visualize the smoothed gene expression dynamics along... |
| plot_QC | Render various plots indicating the tallied gene and cell... |
| plot_transcriptome_summary | Heatmap of the transcriptomic profile. |
| read_counts | Returns a gene expression matrix. |
| remove_cells | Exclude cells from the current dataset |
| remove_clusters | Exclude cells belonging to one or more clusters |
| remove_genes | Exclude genes from the current dataset. |
| remove_outliers | Remove outlier genes and cells. |
| report | Print the current analysis log in the console. |
| sample_size | Returns a contingency table with the counts per type of cell... |
| save_dataset | Save dataset to file. |
| select_dispersed_genes | Select highly-dispersed genes. |
| set_favorite_genes | Store a list of favorite gene names. |
| smooth | Smooth gene expression using the cell state graph |
| test_kernel_widths | Plot cell state graph over different gaussian kernel widths |
