Man pages for igordot/scooter
Streamlined scRNA-Seq Analysis Pipeline
| add_seurat_assay | Add assay to Seurat object. |
| as_data_frame_seurat | Function to extract data from Seurat object. |
| calc_clust_averages | Get cluster averages. |
| calculate_clusters | Run dimensionality reduction, pca, tse, and umap |
| calculate_mito_pct | Calculate mitochondrial percentage from Seurat object. |
| calculate_variance | Get variable genes and scale data. |
| check_identity_column | Check identity of the Seurat object. |
| create_color_vect | Function to create a color vector. |
| create_seurat_obj | Create a new Seurat object from a matrix. |
| differential_expression_global | Calculate differential expression for one group versus all |
| differential_expression_paired | Calculate differential expression between specific groups |
| differential_expression_per_cluster | Calculate differentially expressed genes within each... |
| filter_data | Filter cells based on the number of genes and mitochondrial... |
| geneset_score | Get geneset scores. |
| get_color_scheme | Determine the color scheme. |
| get_dr_point_size | Determine the point size for reduced dimensions scatter plots... |
| get_test_counts_matrix | Get an example counts matrix. |
| import_mtx | Read in 10x Genomics Cell Ranger Matrix Market format data. |
| load_sample_counts_matrix | Read in Gene Expression and Antibody Capture data from a 10x... |
| log_normalize_data | Log normalize data. |
| merge_metadata | Function to merge two metadata tables together. |
| normalize_data | Normalize data |
| pipe | Pipe operator |
| plot_distribution | Plot the distribution of specified features/variables. |
| run_dr | Run dimensionality reduction, pca, tse, and umap |
| run_pca | Run PCA |
| run_tsne | Run TSNE |
| run_umap | Run UMAP |
| save_seurat_counts_matrix | Function to write Seurat counts matrix to csv. |
| sctransform_data | SCT normalize data. |
| set_identity | Set identity of the Seurat object. |
| tidyeval | Tidy eval helpers |
| write_message | Small function to write to message and to log file. |
