Man pages for RyanYip-Kat/yipCat
Some function like ArchR style in Seurat Object
| addSeuratTrajectory | Add a Supervised Trajectory to an Seurat Object |
| ageScore | a function to caculate aging score |
| ArchRHeatmap | function for matrix to doheatmap in archr Style |
| ArchRPalettes | List of color palettes that can be used in plots |
| CalculateRogue | ROGUE calculation |
| calDoubletScores | Add Doublet Scores to an SeuratObject |
| centerRollMean | center mean |
| config | cytof config file for example |
| CPDBDotData | function to prepare data from cellphone output for dot_plot |
| CPDBDotplot | dot plot for cellphone output |
| CPDBHeatmapData | function to prepare data from cellphone output for... |
| CPDBHeatmaps | heatmap plot for cellphone output |
| CustomInteractionScore | function to caculate Interaction score |
| Cytof2Seurat | function to convert cytof data into Seurat |
| DAPlot | Volcano Plot of Difference Analysis Markers |
| deDF | difference markers dataframe for example |
| DetermineK | Calculate the value of the reference factor K |
| DoLikeArchRHeatmap | function doheatmap like DoHeatmap in seurat package |
| dot-batchlapply | batch lapply paralle |
| dot-computeKNN | compute KNN |
| dot-computeLSI | compute LSI(pass) |
| dot-projectLSI | project LSI(pass) |
| dot-safelapply | function to mutiple threads |
| dot-tempfile | create temp file |
| dot-transform10XH5 | transform cutsom matrix into 10X h5 matrix |
| dot-writeCode | write strings into script file |
| EmbPlot | Embeeding plot |
| Entropy | Calculate the expression entropy of each gene |
| entropy_fit | Fit the relationship between expression entropy and mean gene... |
| ent.toli | Remove outlier cells when calculating ROGUE |
| exportCellPhoneDB | a function to export count and metadata for cellphonedb |
| exportEmbCol | a function to export embedding and cloumn to csv file |
| findCellPhoneDB | function to find cellphonedb |
| fixPlotSize | set plot size |
| generateCloupe | run cellranger reanalysis(only for cellranger version 3.1.0) |
| getDoubletsDF | function to filter doublet cells |
| getGroupPval | function to caculate genes in two status's differece... |
| getImputeWeight | get impute weight |
| getSeuratTrajectory | function to get Trajectory Object. |
| ggAlignPlots | Align ggplot plots vertically or horizontally |
| ggGroup | A ggplot-based ridge/violin plot wrapper function |
| ggHex | A ggplot-based Hexplot wrapper function summary of points in... |
| ggOneToOne | A ggplot-based one-to-one dot plot wrapper function |
| GgPlot | function to plot feature Groups |
| ggPoint | A ggplot-based dot plot wrapper function |
| ImputeWeights | function to caculate impute weights |
| installCellphonedb | function to install cellphonedb |
| isDiscrete | whether is discrete |
| makedir | make dir |
| matr.filter | Filtering out low-abundance genes and low-quality cells |
| mergeParams | merge params |
| metascapeBarPlot | metascape GO result left and right plot |
| MyimputeMatrix | impute matrix use impute weights |
| MyplotEmbedding | function to plot Embedding |
| MyplotGroups | function to plot Groups |
| MyplotPDF | function to save plotlist |
| paletteContinuous | continuous paltette color |
| plotSeuratTrajectory | Plot Trajectory after function 'getSeuratTrajectory' |
| quantileCut | function to quantile cut |
| rogue | Calculate the ROGUE value of each putative cluster for each... |
| rogue.boxplot | Visualize ROGUE values on a boxplot |
| scMatrix2CellRangerH5 | code to transform matrix into 10x h5 matrix |
| SE_fun | Identify highly informative genes using S-E model |
| SEplot | S-E plot |
| theme_ArchR | ggplot2 default theme for ArchR |
| wrapperROGUE | Caculate ROGUE values for Cell Cluster and conclude their... |
