| add_cc_score | Quantify cell-cycle activity by phase. |
| add_maehrlab_metadata | Given a Seurat object, add information about our experiments. |
| add_pseudotime_to_seurat | Transfer data from a pseudotime modeling object to a Seurat... |
| add_quadrants | Split a scatterplot (or similar) into quadrants and label... |
| add_rp_mt_percentage | Quantify ribosomal and mitochondrial transcript content cell... |
| add_rp_percentage | Quantify ribosomal transcript content cell by cell. |
| add_tcr | Add T-cell receptor expression from a separate alignment... |
| aggregate_nice | Aggregate data.frame by a categorical variable, permissively. |
| align_embedding_to_reference | Align simple (y-shaped) lineage trees represented as points... |
| annot_ident_plot | Annotate a plot with cluster labels |
| are_compatible | Helper function. Check if a list of markers is compatible... |
| AvailableData | Get available variable names (genes, identity classes, PCA... |
| call_monocle_on_seurat | Extract data from a Seurat object and run Monocle, returning... |
| check_xist_all | Screen for female embryos using simple stats. |
| check_xist_pure | Check for female-specific and male-specific transcripts |
| classify_mlr | Apply a machine learning classifier (from... |
| ClusterBag | Apply a bagged clustering procedure to a Seurat object using... |
| ClusterBagStability | Wrapper for ClusterBag. Measures stability over a range of... |
| cluster_wrapper | A wrapper for Seurat's clustering functions. |
| collapse_by_name | Turn a named list or vector of strings into a pipe-separated... |
| convert_species_dge | Convert a raw digital gene expression matrix from one species... |
| custom_feature_plot | Make tSNE plots (or PCA, or Monocle; it's customizable) |
| custom.make.unique | Consistently label replicates |
| dendrogram_merge_points | Plot a dendrogram and also cut it to merge input into... |
| deseuratify_raw_data | Extract mostly-raw (medium rare?) data from a Seurat object. |
| DESummaryFast | Quickly compute summary statistics for all genes. |
| dge_merge_list | Merge a list of digital gene expression matrices. |
| dir.create.nice | Create new directories recursively and without a warning if... |
| do_enrichr | Programmatically feed gene-sets to Enrichr and save formatted... |
| expected_doublet_counts | Given a named vector x with counts of various cell types,... |
| explore_embeddings | Quickly explore many parameter settings |
| ExploreIteratively | Explore a single-cell dataset, alternating between gene... |
| export_from_seurat | Export raw and normalized data from a Seurat object. |
| faceted_tsne | Plot a dataset's tSNE embedding faceted by experimental... |
| facet_plot_gene_clusters | Draw overlaid line plots of gene clusters from output of... |
| FetchDataZeroPad | FetchData but with zeroes for unavailable genes |
| FillNA | Remove missing values from the metadata, issuing a warning if... |
| FindMarkersFlex | Test for markers flexibly from a Seurat object. |
| fix_cluster_order | Check if a list of cell types is good to be used to order... |
| get_classifier_coefs | Extract coefficients from a glmnet multiclass logistic... |
| get_cTEC_mTEC_genes | Return a table of genes generated by head-to-head comparison... |
| get_macosko_cc_genes | Return cell-cycle genes from original Drop-seq paper by... |
| get_metadata | Get thymus atlas sample metadata. |
| get_mouse_tfs | Maehr lab list of mouse transcription factors. |
| get_ortholog | Return the ortholog of a given gene or NA (if no match).... |
| get_ortholog_nonvec | Return the ortholog of a given gene or NA (if no match). Not... |
| get_ortholog_table | Human-mouse ortholog pairs from Ensembl 87. |
| get_poised_genes | Poised genes from Lesch 2016 Nature Genetics |
| get_preimage | Take in a function from one finite set of strings to another... |
| get_ramilowski | Return human receptor-ligand pairs from Ramilowski et al... |
| get_rene_markers | Return df with handpicked genes. |
| get_similar_genes | Find genes with expression patterns similar to the genes... |
| harmonize_species | Given a gene list and a seurat object, return a gene list... |
| has_ortholog | Same as get_ortholog but returns just T or F. |
| heatmap_gene_clusters | Draw heatmaps of gene clusters from output of... |
| is_mt | Decide if genes are mitochondrial. Currently uses a crude... |
| is_rp | Decide if a gene is a ribosomal subunit or a pre-rRNA... |
| KMeansGapStat | Imitate Seurat::FindClusters but using k-means with the gap... |
| knn_classifier | Classify cells from one Seurat object in terms of another... |
| load_thymus_profiling_data | Load digital gene expression matrices from Maehrlab dropbox. |
| make_heatmap_for_table | Make a heatmap with one column for each cluster in 'unique(... |
| master_pt | Run Monocle, DPT, or PCA-based pseudotime analysis on a... |
| misc_summary_info | Save commonly needed summary plots: plain gray, eday,... |
| normalize_cpx_amt | Rescale every cell to a certain amount of UMIs, where that... |
| outlier_labeled_scatterplot | Return a scatterplot, labeling outliers. |
| pc_as_pt | Take a principal component (first by default) and return a... |
| plot_dendro_with_rect | Plot a dendrogram, labeling merges given by 'converter' with... |
| ProjectCells | Project cells from one Seurat object onto the pseudotime axis... |
| RefineVariableGenes | Update the '@var.genes' slot of a Seurat object using cluster... |
| remove_species_specific_genes | Remove species-specific genes from a Seurat object. |
| remove_TEC_doublets | Remove intra-TEC doublets by finding cells with both a high... |
| replace_with_int_rank | Convert a, b, b, a, c, a to 1, 2, 2, 1, 3, 1. Works with any... |
| SanitizeGenes | Sanitize gene names via 'make.names' |
| save_depth_stats | Assemble very basic summary stats: total UMIs, genes, and... |
| save_feature_plots | Save plots en masse. |
| save_marker_table | Clean and save a df containing columns "gene", "avg_diff",... |
| seuratify_thy_data | Make arrays into Seurat objects. |
| SeuratMerge | Merge two Seurat objects. |
| SeuratPie | Make small-multiple pie charts. |
| smooth_and_cluster_genes | Characterize genes by behavior over pseudotime, returning... |
| strip_suffix | Remove a suffix if it is present, but if it's absent, avoid... |
| strsplit_drop | Wrap base::strsplit with a 'drop' option |
| SubsetDataFlex | Subset data flexibly from a Seurat object. |
| TACS | Make a FACS-like plot from a single-cell rna-seq dataset. |
| text2file | Write text to a file |
| time_series | Return spline-smoothed expression plots over pseudotime. |
| time_series_save | Save plots from 'times_series'. |
| train_save_classifier | Train and save a penalized logistic regression classifier. |
| tsne_colored | Save plots from 'custom_feature_plot'. |
| wheel_plot | Visualize probabilistic classification results |
