Man pages for Jerby-Lab/opipes
What the Package Does (One Line, Title Case)
| apply.formula.HLM | Apply Hierarchical Linear Model with specific formula |
| apply.HLM | HLM, implemented by Christine |
| average.mat.rows | Get the average of each matrix |
| average.mat.rows.parallel | Get the average of each matrix |
| cap_object | Cap Data |
| center.matrix | Matrix centering |
| cluster | Wrapper around sNN clustering in Seurat |
| colMax | Get column maximum |
| colMin | Get column minimum |
| discretize.prvt | Discretize data into Quantiles |
| embed | Wrapper around UMAP and/or TSNE |
| formula.HLM | Execute lmer using formula |
| get.binary.scores | Get Binary Scores |
| get.mat | Get Matrix |
| get.OE | Overall Expression Wrapper |
| get.OE1 | Overall Expression Subroutine |
| get.p.zscores | Convert p-values to z-scores |
| get.top.cor | Fetch genes with top correlation |
| get.top.elements | Fetch top elements of a matrix |
| intersect.list1 | Intersect Lists of Lists |
| labels.mat.2.logical.mat | Labeled Matrix to Logical Matrix |
| prep4OE | Helper function for Overall Expression |
| recon_loss | Reconstruction Loss |
| rgb2hex | RGB to Hexcode |
| rowMax | Get row maximum |
| rowMin | Get row minimum |
| run_pca | Wrapper around PCA |
| sample.per.label | Sample cells per label |
| scale_and_center | Scale and Center |
| scRNA_cluster.annotation.HG | Hypergeometric Test |
| scRNA_cluster.annotation.ttest | Compute _t_-tests |
| scRNA_markers_assign | scRNA Marker Based Cell Type Assignments |
| scRNA_markers_subtype_assign | scRNA Marker Based Cell Type Assignments |
| seuratify | Seuratify your Single Cell Data |
| spatial_sample_visualization | Spatial Cell Mask Visualization |
| spearman.cor | Compute Spearman Correlation on two list objects |
| std_preprocess | Standard single cell RNA preprocessing |
| subsample | Randomly subsample single cell data set |
| subset_list | Subset a list object based on cell ids |
| transfer_data_list_to_so | Transfer meta data from a list object to a Seurat object. |
| t.test.mat | HLM, implemented by Christine |
| umap_tsne | Wrapper around UMAP and/or TSNE |
| var_explained_seurat | Variance Explained |
