Man pages for jacobheng/cellwrangler
Supplemental toolkit for single-cell RNAseq analysis
| annotate_bcv | Calculate and annotate biological coefficent of variation |
| calculate_mt_exprs | Calculate mitochondrial gene expression |
| CellType_genes_jitter | Plot gene expression for all CellTypes as jitter plots |
| create_monocle_cds | Create a monocle CellDataSet object from a directory of... |
| createMultiSoupChannel | Create multiple Soup Channels from an cellranger-aggregated... |
| CreateSeuratObjectList | Create a list of Seurat Objects |
| createSoupChannel | Create a single Soup Channel |
| dim_coord_barcode | Find rownames of cells from coordinates of dimensionality... |
| emptySoup | Estimate expression profile of soup from empty droplets |
| exprs_threshold | Determine if cells are above an expression threshold of a... |
| find_CCA_genes | Find high variance genes for CCA |
| findGeneID | Find Ensembl gene IDs given gene names |
| findGeneName | Find gene names given Ensembl gene IDs |
| find_highbcv_genes | Find genes with high biological coefficent of variation |
| findRows | Find rows by row names |
| find_sample_dispersed_genes | Find dispersed genes in each sample in CellDataSet |
| find_sample_expressed_genes | Find expressed genes in each sample in CellDataSet |
| fit_cds_vglm | Fit vector generalized linear model to a CellDataSet object |
| gene_barplot | Plot mean gene expression as bar plot |
| gene_jitterplot | Plot expression of cells as jitter plot |
| get_expressed_genes | Find genes expressed in a CellDataSet object |
| get_kegg_database | Get kegg database for an organism |
| get_kegg_pathway_genes | Get genes for a kegg pathway |
| get_mean_condition_counts | Get mean read counts for cells belonging to a condition |
| get_patternMarkerNames | Get pattern markers as gene names for a set of CoGAPS results |
| load_10X_matrix | Load an expression matrix from a directory of... |
| load_CoGAPS_res | Load a set of CoGAPS results |
| log_normalize_cds | Normalize and log monocle cds |
| make_rnk | Make rank lists |
| mean_scale_cds | Mean scale expression of cell groups across multiple samples... |
| merge_by_rownames | Merge dataframes or matrices by rownames |
| merge_df_list | Merge a list of dataframes or matrices |
| monocle_fitModel | Fit model function in monocle |
| monocle_sparse_prcomp_irlba | Sparse prcomp irlba implemented in Monocle 3 alpha |
| monocle_UMAP | Uniform Manifold Approximation and Projection in Monocle 3... |
| order_marker_matrix | Order expression matrix of marker genes by cell group |
| plot_bcv | Plot biological coefficent of variation and annotate genes |
| plot_CoGAPS_ChiSq | Plots the mean ChiSq values of a set of CoGAPS results |
| plot_CoGAPS_pattern_cor_dendrogram | Plot CoGAPS pattern correlation dendrogram |
| plot_CoGAPS_pattern_cor_heatmap | Plot CoGAPS pattern correlation heatmap |
| plot_CoGAPS_pattern_dim | Plot CoGAPS pattern on a dimensionality reduction plot |
| plot_CoGAPS_patternSet_dim | Plot a set of CoGAPS patterns on a dimensionality reduction... |
| plot_drops_diagnostics | Plot diagnostic plot for testDrops results |
| plot_gene_exprs | Plot gene expression in cells |
| plot_groups | Plot cell groups |
| plot_marker_heatmap | Plot heatmap of marker genes ordered by cell group |
| plot_matrix_dendrogram | Plot a clustered dendrogram |
| plot_matrix_heatmap | Plot a clustered heatmap |
| plot_mean_exprs_heatmap | Plot mean expression heatmap |
| plot_pathway_dendrogram | Plot pathway dendrogram |
| plot_pathway_heatmap | Plot pathway heatmap |
| plot_pheatmap | Plot pheatmap object |
| plot_sparse_pca_var | Plot variance explained by sparse PCA |
| rowSD | Get standard deviation for rows in a matrix |
| rowSE | Get standard error of the mean for rows in a matrix |
| sparse_pca | Perform sparse pca on a matrix |
| sparse_pca_biplot | Plot biplot for sparse pca |
| spectral_tsne | Reduce dimensions of a matrix with pca and tSNE |
| spectral_umap | Reduce dimensions of a matrix with pca and UMAP |
| split_aggr_mtx | Split a cellranger-aggregated matrix into multiple matrices... |
| subset_cds | Subset cds by cell group |
| summarize_cds_exprs | Get gene-level summary statistics for CellDataSet object |
| testDrops | Determine whether droplets are cells or blank drops in an... |
