Man pages for NCBI-Hackathons/RClusterCT
Classifier for Single-cell RNA-seq Using Cell Clusters
| append_genes | Given a reference matrix and a list of genes, take the union... |
| assess_rank_bias | Find rank bias |
| assign_ident | manually change idents as needed |
| average_clusters | Average expression values per cluster |
| binarize_expr | Binarize scRNAseq data |
| build_atlas | Function to combine records into single atlas |
| calc_distance | Distance calculations for spatial coord |
| calc_similarity | compute similarity |
| calculate_pathway_gsea | Convert expression matrix to GSEA pathway scores (would take... |
| call_consensus | get concensus calls for a list of cor calls |
| call_to_metadata | Insert called ident results into metadata |
| cbmc_m | reference marker matrix from seurat citeseq CBMC tutorial |
| cbmc_ref | reference matrix from seurat citeseq CBMC tutorial |
| check_raw_counts | Given a count matrix, determine if the matrix has been either... |
| clustify | Compare scRNA-seq data to reference data. |
| clustify_lists | Main function to compare scRNA-seq data to gene lists. |
| clustify_nudge | Combined function to compare scRNA-seq data to bulk RNA-seq... |
| clustifyr_methods | Correlation functions available in clustifyr |
| clustifyr-package | clustifyr: Classifier for Single-cell RNA-seq Using Cell... |
| collapse_to_cluster | From per-cell calls, take highest freq call in each cluster |
| compare_lists | Calculate adjusted p-values for hypergeometric test of gene... |
| cor_to_call | get best calls for each cluster |
| cor_to_call_rank | get ranked calls for each cluster |
| cor_to_call_topn | get top calls for each cluster |
| cosine | Cosine distance |
| downrefs | table of references stored in clustifyrdata |
| downsample_matrix | downsample matrix by cluster or completely random |
| feature_select_PCA | Returns a list of variable genes based on PCA |
| file_marker_parse | takes files with positive and negative markers, as described... |
| find_rank_bias | Find rank bias |
| gene_pct | pct of cells in each cluster that express genelist |
| gene_pct_markerm | pct of cells in every cluster that express a series of... |
| get_best_match_matrix | Function to make best call from correlation matrix |
| get_best_str | Function to make call and attach score |
| get_common_elements | Find entries shared in all vectors |
| get_similarity | Compute similarity of matrices |
| get_ucsc_reference | Build reference atlases from external UCSC cellbrowsers |
| get_unique_column | Generate a unique column id for a dataframe |
| get_vargenes | Generate variable gene list from marker matrix |
| gmt_to_list | convert gmt format of pathways to list of vectors |
| human_genes_10x | Vector of human genes for 10x cellranger pipeline |
| insert_meta_object | more flexible metadata update of single cell objects |
| kl_divergence | KL divergence |
| make_comb_ref | make combination ref matrix to assess intermixing |
| marker_select | decide for one gene whether it is a marker for a certain cell... |
| matrixize_markers | Convert candidate genes list into matrix |
| mouse_genes_10x | Vector of mouse genes for 10x cellranger pipeline |
| not_pretty_palette | black and white palette for plotting continous variables |
| object_data | Function to access object data |
| object_loc_lookup | lookup table for single cell object structures |
| object_ref | Function to convert labelled object to avg expression matrix |
| overcluster | Overcluster by kmeans per cluster |
| overcluster_test | compare clustering parameters and classification outcomes |
| parse_loc_object | more flexible parsing of single cell objects |
| pbmc_markers | Marker genes identified by Seurat from single-cell RNA-seq... |
| pbmc_markers_M3Drop | Marker genes identified by M3Drop from single-cell RNA-seq... |
| pbmc_matrix_small | Matrix of single-cell RNA-seq PBMCs. |
| pbmc_meta | Meta-data for single-cell RNA-seq PBMCs. |
| pbmc_vargenes | Variable genes identified by Seurat from single-cell RNA-seq... |
| percent_clusters | Percentage detected per cluster |
| permute_similarity | Compute a p-value for similarity using permutation |
| plot_best_call | Plot best calls for each cluster on a tSNE or umap |
| plot_call | Plot called clusters on a tSNE or umap, for each reference... |
| plot_cor | Plot similarity measures on a tSNE or umap |
| plot_cor_heatmap | Plot similarity measures on heatmap |
| plot_dims | Plot a tSNE or umap colored by feature. |
| plot_gene | Plot gene expression on to tSNE or umap |
| plot_pathway_gsea | plot GSEA pathway scores as heatmap, returns a list... |
| plot_rank_bias | Query rank bias results |
| pos_neg_marker | generate pos and negative marker expression matrix from a... |
| pos_neg_select | adapt clustify to tweak score for pos and neg markers |
| pretty_palette | Color palette for plotting continous variables |
| pretty_palette2 | Color palette for plotting continous variables, starting at... |
| pretty_palette_ramp_d | Expanded color palette ramp for plotting discrete variables |
| query_rank_bias | Query rank bias results |
| ref_feature_select | feature select from reference matrix |
| ref_marker_select | marker selection from reference matrix |
| reverse_marker_matrix | generate negative markers from a list of exclusive positive... |
| run_clustifyr_app | Launch Shiny app version of clustifyr, may need to run... |
| run_gsea | Run GSEA to compare a gene list(s) to per cell or per cluster... |
| sce_pbmc | An example SingleCellExperiment object |
| seurat_meta | Function to convert labelled seurat object to fully prepared... |
| seurat_ref | Function to convert labelled seurat object to avg expression... |
| so_pbmc | An example Seurat object |
| vector_similarity | Compute similarity between two vectors |
| write_meta | Function to write metadata to object |
