Man pages for fmicompbio/swissknife
Handy code shared in the FMI CompBio group
| addUtilsFunctions | Copy utility functions to package |
| annotateRegions | Annotate regions. |
| calcAndCountDist | Count frequency of differences between values in integer... |
| calcPhasogram | Calculate phasograms (same strand alignment distances). |
| col2hex | Get hex color |
| dot-getDistMat | Get Distances between 2D Points and a Loess Fit |
| dot-isValidColor | Check for valid color specification. |
| estimateNRL | Estimate the nucleosome repeat length (NRL) from a phasogram. |
| getGenomicTiles | Get regions tiling a genome. |
| getInsertSizeDistFromBam | Tabulate insert sizes from paired-end alignments in bam... |
| getMappableRegions | Get mappable regions of a genome. |
| labelCells | Assign labels to cells using known marker genes |
| loadExampleData | Access example data |
| normGenesetExpression | Calculate normalized expression of a gene set |
| parsePkgVersions | Parse R and R package versions from session informations |
| plotBitScatter | Create a bitmap-rendered plot. |
| plotGeneRegion | Plot gene region |
| plotPhasogram | Plot annotated phasogram. |
| plotSelVarGenes | Plot Selected Variable Genes |
| prepareGTF | Prepare GTF file for use with plotGeneRegion |
| readSampleTsvs | Read sample tsv files from seqdata storage |
| sampleControlElements | Sample control elements that match a target distribution. |
| selVarGenes | Select Variable Genes in Single Cell RNA-seq |
| specificityScore-methods | Calculate gene-expression specificity scores. |
| swissknife-package | swissknife - handy code shared in the FMI CompBio group |
| valueToColor | Map numerical values to colors. |
| weightedMeanByID | Aggregate different rows assigned to the same ID by... |
