Man pages for hesselberthlab/scrunchy
Single Cell Reconstruction of Functional Heterogeneity
| add_label | Adds useful labels to colData. |
| add_stats | Add stats to plot activities per cluster |
| calc_cell_cycle | Calculate cell-cycle assignments |
| calc_hairpin_coverage | Calculate coverage across hairpins |
| calc_pca | Calculate principal components using irlba |
| calc_qvalues | Calculate q-values |
| calc_tsne | Generate 2D cell embeddings using tSNE |
| calc_umap | Generate 2D cell embeddings using UMAP |
| calc_var_features | Calculate variable features |
| clr_normalize | Centered log-ratio normalize a matrix |
| cluster_kmeans | Run k-means clustering algorithm |
| cluster_leiden | Run Leiden clustering algorithm |
| create_fsce | Create a functional single-cell experiment |
| create_sce_feature | Create a single-cell feature experiment |
| create_sce_haircut | Create a single-cell Haircut experiment |
| create_sce_rnaseq | Create a single-cell mRNA-seq experiment |
| filter_matrix | Filter and write a sparseMatrix keeping only specified... |
| filter_molecules | Filter barcodes in molecule file and write to disk |
| fsce_small | An example FunctionalSingleCellExperiment |
| fsce_tidy | Tidied tibble of data from fsce_small |
| FunctionalSingleCellExperiment | Constructor for a 'FunctionalSingleCellExperiment' object |
| FunctionalSingleCellExperiment-class | An S4 class to represent a functional single cell experiment |
| human_gene_ids | Human gene identifiers |
| is.molecule_df | Test if the object is a molecule_df. |
| log_normalize | Log-normalize a matrix |
| molecule_df | data.frame that contains molecule info |
| normalize | Normalize data in a SingleCellExperiment |
| palette_OkabeIto | Color palette proposed by Okabe and Ito |
| pbmc_marker_genes | Comman human PBMC marker genes |
| plot_activity | Plot activities per cluster |
| plot_barcodes | Plot UMI count distribution for barcodes |
| plot_dims | Scatter plot of cells in a two-dimensional embedding. |
| plot_dims_multi | Plot multiple 2D plots in a grid |
| plot_hairpin_coverage | Plot coverage across hairpins |
| plot_heatmap | Heatmap of signals |
| plot_pcvariance | Plot PCA variance |
| plot_saturation | Plot sequencing saturation |
| read_matrix | Load mtx formatted 10x or haircut matrices |
| read_molecules | Read molecule file into memory |
| scale_OkabeIto | Okabe-Ito color scale |
| scrunchy | scrunchy: single-cell reconstruction of functional... |
| scrunchy_data | Provide path to scrunchy internal data |
| stat_activity_grouped | Compare activity differences between groups. |
| stat_anova_grouped | Analysis of variance of activities across groups |
| stat_anova_tukey | Post-hoc analysis of ANOVA results |
| tidy_all | Tidy all |
| tidy_coldata | Tidy colData |
| tidy_counts | Tidy counts data |
| tidy_dims | Tidy reducedDims data |
| tidy_logcounts | Tidy logcounts data |
| tidy_stats_grouped | Tidy grouped statistics |
| umitools_to_mtx | Convert umitools flat format tsv to sparseMatrix .mtx format |
| write_matrix | Write a sparseMatrix to disk |
