Man pages for HuobinTan/scVAT
Single Cell Visualization Analysis Toolkit
| addCellProp | Add cell properties |
| addGeneProp | Add gene properties |
| addPropMeta | Add meta feature |
| buildKNNGraph | Building kNN Graph for clustering |
| clusterGraph | Clustering Graph |
| doAllDiffAnalysis | Differential Analysis for specific clusters (according to... |
| doCluster | do Unsupervised Clustering using kNN-graph |
| doDESeq2Test | call DESeq2 test for differential analysis |
| doDiffAnalysis | Differential Analysis for group1 and group2 (according to... |
| doPCA | do PCA using irlba library |
| doTSNE | do tSNE using Rtsne library |
| doTTest | do t-test for differential analysis |
| doWilcoxTest | do Wilcox Rank Sum test for differential analysis |
| filterCells | Filter cells |
| filterGenes | Filter genes |
| getAnalysisColName | Get the analysis key's colnames |
| getAnalysisColnames | get availbale analysis data colnames |
| getAnalysisData | Get analysis data result |
| getAnalysisKey | get available analysis key name |
| getAnalysisList | Get analysis list |
| getCellPropData | Get cell properties |
| getGenePropData | Get gene properties |
| getPropMeta | Get the property meta features |
| getUseData | Get dataset |
| initVATEntity | initialize VAT Entity |
| load10XH5 | load data from H5 file |
| load10XPath | load data from 10x path (including barcodes.tsv, genes.tsv... |
| loadAnalysis | load analysis result manually |
| loadAnalysisFromCSV | load analysis result manually from csv |
| loadCSVData | load data from csv file |
| plotAnalysis | plot using analysis data |
| plotGene | plot gene expression based on the analysis result |
| plotGenes | plot some gene expressions (sometime show many plots) based... |
| plotPC | plot PC maps #' |
| plotPCASDev | Plot some analysis data's Standard Deviation (such as PCA) |
| plotThreeGenes | plot three gene expression based on the analysis result at a... |
| plotTSNE | plot tsne maps |
| plotTwoGenes | plot two gene expression based on the analysis result at a... |
| saveVATToCSV | Save VAT data or analysis result |
| setGenePercent | Calculating the expression's percent for some pattern's genes |
| show-methods | show method for VATEntity |
| startVATGUI | Graphical User Interface for Single-Cell Visual Analysis... |
| VATEntity | The VAT Entity Class |
