![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
| avgGeneCat | Average Category Gene Expressions |
| cn_barplot_grnSing_base | barplot this specific GRN |
| cn_classAssess | Assess classifiers based on validation data |
| cn_clPerf | determine performance of classification at given threshold |
| cn_computeAUCPR | compute AUPCR |
| cn_correctZmat | make Inf and -Inf values sensible |
| cn_eval | run cn_clPerf across thresholds |
| cn_findSensAt | return the sens at given FPR |
| cn_rectArea | compute area of rect given by |
| compareGenePairs | Compile genePairs comparison matrix |
| csRenameOrth | enable cross-species comparison |
| downSampleW | weighted subtraction from mapped reades |
| extractSCE | extract sampTab and expDat sce object into regular S3 objects |
| extractSeurat | extract sampTab and expDat seurat object into regular S3 objects |
| findAvgLabel | Make training label |
| findBestPairs | finds the best pairs to use |
| findClassyGenes | Find Classifier-Worthy Gene Candidates |
| GEP_makeMean | row average (or median) based on groups |
| getClassGenes | Find Classy Genes |
| getSpecGenes | get the genes specific to each diffexp in a list of them |
| gnrAll | find genes higher in a cluster compared to all other cells |
| gnrBP | find best pairs |
| harmonize | harmonize data sets |
| hm_enr | heatmap of the enrichment result |
| hm_gpa_sel | heatmap genes and groups |
| load10x | Loads 10x data mtx |
| makeGeneCompareTab | Make Gene Comparison Table |
| mclust_Mat | run Mclust on an expression matrix |
| mergeLoad10x | Loads 10x data mtx |
| pair_transform | makes complete gene-to-gene comparison |
| pca_to_tsne | make tsne from pca |
| plotDBscan | plot tsne results |
| plotGeneComparison | Gene expression plotting |
| plotGPApca | plot gpa res |
| plot_class_PRs | Plot results of sc_classAssess |
| probTrans | transform mclust class res to expression prob estimates |
| ptGetTop | Find the best gene pairs for training |
| query_transform | makes complete gene-to-gene comparison |
| randomize | randomize data matrix |
| reorderCellsByGrp | re-order cells for plotting |
| rf_classPredict | classify samples |
| scn_extract_SN_DF | returns a DF of: sample_id, description, ctt, subnet_name, score |
| scn_make_tVals | Estimate gene expression dist in CTs |
| scn_netScores | GRN status |
| scn_normalizeScores | Normalize grn status as compared to training data |
| scn_predict | Predict query using broad class classifier |
| scn_rawScore | computes the raw score for a gene as xmax-abs(zscore). |
| scn_score | GRN status |
| scn_train | Training |
| scn_trainGRN | Figure out normalization factors for GRNs, and norm training data |
| sc_Accu | Assess classifiers based on validation data |
| sc_classAssess | assess the classifiers performance based on validation data |
| sc_classThreshold | determine performance of classification at given class threshold |
| sc_filterCells | find cells that pass criteria |
| sc_filterGenes | find genes that pass criteria |
| sc_findEnr | finds genes higher in one group vs others |
| sc_hmClass | heatmap of the classification result |
| sc_makeClassifier | Make Classifier |
| sc_trans_rnaseq | weighted subtraction from mapped reades and log applied to all |
| skylineClass | Skyline waterfall |
| tsneMultsimp | plot tsne and genes |
| utils_loadObject | loads an R object when you don't know the name |
| utils_myDate | print date |
| utils_myDist | 1-PCC distance |
| utils_stripwhite | strip whitespace from a string |
| utils_strip_fname | reduces full path to filename |
| weighted_down | weighted subtraction from mapped reades, applied to all |