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_kegg_database | Get kegg database for an organism |

get_kegg_pathway_genes | Get genes for a kegg pathway |

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 |

merge_by_rownames | Merge dataframes or matrices by rownames |

merge_df_list | Merge a list of dataframes or matrices |

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_drops_diagnostics | Plot diagnostic plot for testDrops results |

plot_gene_exprs | Plot gene expression in cells |

plot_groups | Plot cell groups |

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_pattern_cor_dendrogram | Plot pattern correlation dendrogram |

plot_pattern_cor_heatmap | Plot pattern correlation heatmap |

plot_pattern_dim | Plot pattern on a dimensionality reduction plot |

plot_patternSet_dim | Plot a set of patterns on a dimensionality reduction plot |

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_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... |

summarize_cds_exprs | Get gene-level summary statistics for CellDataSet object |

testDrops | Determine whether droplets are cells or blank drops in an... |

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