Man pages for zzwch/convgene
This package is designed to conveniently convert gene between human and mouse.
| CheckBrewerPal | Check pal in brewer |
| CheckDuplicate | Check Function |
| CheckFeatures | Check Feature Duplicate and Not In Data |
| color2RGB | convert a color name to RGB character |
| ConvertHomoGene | convert genes symbols between organisms |
| dropColors | drop unused colors |
| exportUMIByBatch | export UMI to each file by each Batch |
| InferScaleFactor | Infer the scale factor used for normalization |
| inferUMI | Infer UMI from scale-factor-normalized data |
| IsNULLorNA | check NULL or NA |
| list2df | convert a list of vectors with different lenght to data.frame |
| Message | format a text message |
| pl_averageHeatmap | Heatmap of average expression of select features |
| pl_dimplot | Dimensional reduction plot |
| pl_dotplot | Use dotplot/bubbleplot to visualize average/median and... |
| pl_heatmap | plot heatmap using pheatmap |
| pl_rastrFeaturePlot | rastr version of partial FeaturePlot |
| pl_scatterplot | plot x-y scatters |
| pl_segmentPlot | Plot the expression of one gene using bar/vline, or so called... |
| pl_slingshot | DimPlot and Slingshot curves |
| pl_splitDimplot | plot multiple DimPlot for each batch |
| pl_stackedViolinPlot | stacked Violin Plots in one plot |
| pl_tableHeatmap | Heatmap of a 2D-table |
| pl_vioboxplot | Voinlin and Boxplot in one plot |
| pp_annotateHashtagSeurat | Annotate seurat data derived by pp_hashtagDemultiplex... |
| pp_centerData | Scale data in each group |
| pp_fastMNN | A wrapper function to quickly run fastMNN using... |
| pp_findVariableFeatures | Find variable features across batches |
| pp_hashtagDemultiplex | render rmarkdown file for de-multiplex hash-tag data of... |
| pp_preprocess | A wrapper function to quickly run standard processing... |
| pp_runHarmony | A Wrapper of harmony::RunHarmony |
| pp_seuratV3Integration | A wrapper function to quickly run fastMNN using... |
| readRda | load saved RData |
| RobustRescale | similar to scales::rescale but use quantile 95 |
| rowSmooth | smooth each row of matrix |
| scanpy_colors | discrete colors imported from scanpy.pl.palettes |
| SetDefaultAes | update data.frame with new name added |
| setSummary | set calculations |
| SignCorrectionByCor | Correct sign by correlation |
| str_to_char | convert string into a vector of each char |
| str_to_gene | convert string vector to list/vector of genes |
| SubsetDataAndGroup | Subset Data and Group |
| SummariseDataByGroup | calculate average/median and percentage expression of... |
| SummariseExpr | Do summarise (e.g. mean) for a given vector |
| tl_calcFeatureScore | calculate average/median rescale expression of features (eg.... |
| tl_calcSimilarity | calculate inter-similarity or intra-similarity of clusters |
| tl_crossTableEnrichment | statistics of cross table |
| tl_GeneSetScore | Gene Set Scores |
| tl_PairwiseDEGs | clac DEGs among multiple groups |
| tl_RunPCAScore | a robust PCA for Seurat |
| tl_RunSlingshot | a wrapper of slingshot |
| umi2tpm | normalize UMI matrix to TPM |
| vectorSmooth | smooth a vector |
| write_clip | Write clipboard |
| write_dataToJavaGSEA | write GSEA files |
| write_genesToMeatascape | a helper function to write files for metascape analysis. |
| write_seuratToScenic | write SCENIC data for in-house scenic-pureR |
