Man pages for AlexanderKirchmair/datamisc
Various functions for data handling
| add_level | Add new levels to a factor |
| baseext | File extension of path |
| body | Return the middle n rows and columns of an object |
| ce | Combine character values into a vector or list without quotes |
| cjoin | Cbind multiple matrices by shared rownames |
| clusterData | Hierarchical clustering of data |
| col2rownames | Column to rownames |
| collapse | Collapse duplicate ids |
| colorcat | Print in color |
| compareDF | Colored printing to compare two dataframes |
| convertGeneIDs | Gene ID conversion |
| convertGeneSets | Convert gene sets between different formats |
| convertGeneSpecies | Convert gene IDs between species |
| correl | Calculate correlations between any types of variables |
| COX | Cox Proportional Hazards Analysis |
| cutstr | Limit number of characters in a string |
| cxheatmap | Heatmap plotting with ComplexHeatmap |
| dbugapply | Drop-in replacement for lapply to quickly identify all... |
| dedupl | Rename duplicated strings |
| download | Download file from url |
| expand | Expand (demultiplex) rows with multiple ids |
| find_markers | Find markers for groups in a Seurat object |
| fp | File path |
| genPalettes | Generate distinct color palettes |
| getBiomaRt | Retrieve data from BiomaRt |
| getColors | Generate color mappings for discrete data columns in a... |
| get_feature_ranks | Get feature ranking vector from differential abundance... |
| getGEOdata | Get data from the GEO database |
| getGOgenes | Get GO gene sets |
| getMetabolicAtlas | Get gene/metabolite sets from metabolicatlas |
| getMitoCarta | Get gene sets from MitoCarta3 |
| getMSigDB | Get gene sets from msigdbr |
| getPaletteer | Select colors using the 'paletteer' package |
| getRanks | Get feature ranks from differential abundance testing |
| get_seu_dataset | Load Seurat datasets |
| get_top_markers | Extract top markers from find_markers() results |
| ggbar | Barplots with ggplot2 |
| ggdesign | Plot colData/experimental design matrix |
| ggpca | Principal component analysis and plotting of data |
| ggpdf | Save ggplot as pdf |
| ggpng | Save ggplot as png |
| ggseabar | GSEA bar plot |
| ggstat | Ggplot with errorbars |
| ggtopfeatures | Barplot of the top features of an expression matrix |
| ggvolcano | Volcano plots using ggplot2 |
| gradient | Get color gradients |
| grapes-less-than-L-greater-than-grapes | List assignment pipe |
| grapes-less-than-P-greater-than-grapes | Parallel list assignment pipe |
| grapes-less-than-Q-greater-than-grapes | SGE qsub list assignment pipe |
| grapes-less-than-S-greater-than-grapes | List assignment pipe |
| grapes-L-greater-than-grapes | List pipe |
| grapes-P-greater-than-grapes | Parallel list pipe |
| grapes-Q-greater-than-grapes | SGE qsub list pipe |
| grapes-S-greater-than-grapes | List pipe |
| gseaplot | GSEA plot modified from 'enrichplot::gseaplot2' |
| head2 | Return the first n rows and columns of an object |
| intercalate | Intercalate one vector with another |
| intersection | Intersection of all elements |
| KM | Kaplan-Meier Survival Analysis |
| lgrep | Pattern Matching and Replacement |
| listpipe | List pipe function |
| make_filenames | Safe filenames |
| matScale | Scale rows (columns) of a matrix |
| mkdir | Make directory |
| naf | Set NA values to FALSE |
| napply | Nested apply |
| nar | Set NA values to any other value |
| na_skip | Skip rows/columns containing NA values |
| nat | Set NA values to TRUE |
| nf_summary | Import and plot preprocessing statistics from nf-core/rnaseq... |
| nf_tximport | Import counts from nf-core/rnaseq pipeline using tximport |
| nf_versions | Get versions of tools used in the nf-core/rnaseq pipeline |
| padjust | Adjust P-values for Multiple Comparisons |
| partition | Divide vector into n groups |
| pickColors | Interactive color picker |
| pipe | Pipe operator |
| pval_format | Format p-values for printing |
| qapply | SGE qsub wrapper function |
| quo_class | Get class of a quoted object |
| rangescale | Scale data within range |
| rdataframe | Generate a random data.frame |
| readGMT | Read GMT files |
| readGTF | Read gtf files |
| readTables | Read all sheets from .xlsx file |
| rgenes | Get random genes |
| rjoin | Rbind multiple matrices by shared colnames |
| rlist | Generate a random list |
| rmat | Generate a matrix of random numbers |
| rounddown | Rounding of numbers |
| roundup | Rounding of numbers |
| rownames2col | Rownames to column |
| runDESeq2 | Differential expression analysis with DESeq2 |
| runfGSEA | GSEA with fGSEA |
| runGSEA | GSEA with clusterProfiler |
| runGSVA | Single-sample gene set enrichment with GSVA |
| runLIMMA | Differential expression analysis with LIMMA |
| runORA | Gene set over-representation analysis |
| runTEST | Differential expression analysis with custom test |
| saveplot | Save plot to file |
| setColnames | Set the Names in an Object |
| setRownames | Set the Names in an Object |
| seu_dotplot | DotPlot wrapper for Seurat |
| seu_downsample | Downsample Seurat object |
| seu_umap | UMAP plot wrapper for Seurat |
| showColors | Display colors in console |
| size | Memory size of workspace objects |
| sourcelib | Source R functions from dir into local env |
| sourceRMD | Source R code of an RMD file |
| stratify | Stratify variables based on quantiles |
| stratify_var | Stratify helper function |
| subInf | Replace Inf values for plotting |
| summarise_cols | Summarise multiple columns by grouping |
| summarise_rows | Summarise multiple rows by grouping |
| theme_basic | Basic ggplot2 theme |
| theme_dev | Ggplot2 theme for checking plot layout and margins |
| uniqueSets | Get unique sets (irrespective of item order) |
| versionInfo | Software version reporting |
| writeGMT | Write GMT files |
| writeTables | Write dataframes to .xlsx file |
