Man pages for MyersGroup/testisAtlas
testisAtlas: R functions and analysis scripts used in the analysis of testis single cell RNAseq
| binned_mean_regprob | Calculate mean regulation probabilities for binned genes for... |
| clustered_heatmap | Clustered heatmap (partially deprecated) |
| compare_factorisations | Plot correlation heatmap comparing two sets of loadings |
| component_enrichment | Calculate enrichment for a set of genes for each component |
| correlate_regprobs | For a matrix of genes by motifs, calculate correlations |
| create_grob_list | Create list of grobs from a function and input |
| dmultinom_v | Vectorised multionimial distribution |
| download_flank_sequences | Download sequences flanking gene |
| download_tss | Download location of Transcripion Start Sites from Ensembl... |
| export_all_pwms | Export PWMs in MEME format |
| export_FASTA | Export sequences to file in FASTA format |
| expression_dt | Create data table of gene expression for a subset of genes |
| find_motifs_parallel | For known motifs, run MotifFinder to find motif presence... |
| gene_expression_pseudotime | Create long data table of gene expression for a subset of... |
| gene_list | Print list of genes in component and their annotations |
| get_component_motifs | For an SDA component, find motifs /de novo/ |
| get_density | Calculate 2D density |
| get_top_genes | Find the top x genes for a component |
| GO_enrichment | Perform Gene Ontology (Biological Process) enrichment... |
| go_volcano_plot | Volcano plot of gene ontology enrichment resultd |
| imputed_vs_raw | Plot gene expression through pseudotime (Raw & Imputed) |
| load2 | Save R Objects, as multiple files in a folder |
| load_component_orderings | Load component orderings in global environ |
| load_curve_data | Load Curve Data |
| log_colour_scale | Calculate log colour scale |
| manhatten_plot | Plot Manhatten Style Enrichment for each component |
| match_cells2 | Find pairs of cells that are close in tSNE space |
| mean_prob_bycomp | DEPRECATED, only use if you want custom number of n, For a... |
| melt_genes | Create long table combining gene expression and cell metadata |
| Mode | Find mode of values |
| motif_consensus | Extract matrix of motif occourences from sequence_matrix |
| plotCellAUC | Plot ROC curve for imputation rankings |
| plot_cell_scores | Plot scores |
| plot_component_regprobs | plot regprobs within binned components |
| plot_meanprob_bycomp | Plot meanprob over components |
| plot_motif_matches | For denovo motif and known motif, plot sequence logos |
| plot_pseudotime_expression_panel | Plot pseudotime expression panel |
| princurve_bootstrap | Bootstrap Principal Curve Analysis |
| print_loadings_scores | Plot gene loadings with cell scores underneath |
| print_pca | Print PCA |
| print_raw_tsne | Print tsne based on raw expression rather than SDA scores |
| print_tsne | Plot tSNE |
| ptorder | Order Components by PseudoTime |
| reverse_normalisation | Reverse DGE Normalisation |
| rotate_matrix | Generate rotation matrix / rotate a matrix |
| rotate_SDA | Rotate SDA factorisation |
| rotate_tsne | Rotate a tSNE embedding about the origin |
| save2 | Save R Objects, as multiple files in a folder |
| sda_predict | Compute Imputed Expression values |
| sequence_matrix | Create matrix representation of sequences with highlighted... |
| single_component_enrichment | Calculate enrichment for a set of genes in a single component |
| sort_matrix | Sort matrix to highest correlations are along the diagonal |
| split_loadings | Split SDA components into positive and negative components |
| ternaryColours | Plot tricolor tSNE |
| tricolour_tsne | Plot tricolor tSNE |
