Man pages for mumichae/DASSIE
Detection of Alternative Transcription Start Sites
| AutoIGV | Function to produce IGV session files and screenshorts... |
| copyODS | Make a clean copy of the original ODS |
| coverageMatrix | Coverage Matrix |
| coverageMatrixPerSite | Coverage Matrix per Site |
| coverage_ratio | for checking the coverage |
| drawCoverageHeatmap | Draw a heatmap |
| extend | Extend regions upstream or downstream |
| featureInfo | Retrieve info as data.table |
| generalise_gene_type | Summarise gene type |
| get_all_results | Get all OUTRIDER results |
| getDassieRegions | Extract regions around TSS and PAS and returns a GRanges... |
| getExonsDt | Get exons from txdb |
| gr_to_bed | converts GRanges object to bed file |
| injectFeatures | Take random features and replace these in simulated |
| injectSample | Inject a complete sample from shifted ods into original ods |
| multiplotLoop | Plot multiple results with a loop |
| pasRegions | Polyadenylation site regions |
| plotCoverageHeatmap | Visualise coverage for multiple genes using average counts |
| plot_exon_coverage | gene_type must be included in counts data table |
| plot_exon_distribution | plots number of exons according to gene type |
| plotExpressionRank2 | Expression Ranks with marked sample |
| plot_mean_counts | Boxplots the distribution of mean counts per gene compared... |
| plotPerSiteCoverageHeatmap | Coverage Heatmap per site |
| plotQQ2 | QQ plots with marked samples |
| PrintAnnotationHeader | PrintAnnotationHeader Prints header of the annotation part to... |
| PrintAnnotationTrack | PrintAnnotationTrack Prints annotation tracks to the session... |
| PrintIGVbatch | Prints IGV batch script file for further png profuction |
| PrintIGVSessionHeader | PrintIGVSessionHeader Prints session header with coordinates... |
| PrintIGVSessionResourses | PrintIGVSessionResourses Prints session resourses with paths... |
| PrintIGVTrack | PrintIGVTrack Prints tracks of bams to the session file |
| ProduceIGVSession | ProduceIGVSession Produces session file for 1 entry of coords... |
| removeZeroCounts | Remove simulated 0-count rows |
| set_AutoIGV_DEBUG | toogles the debuging mode for AutoIGV on and off |
| SetHeigthAndClose | SetHeigthAndClose Sets up equal heiths to the IGV tracks |
| shift | Shift regions upstream or downstream |
| simulatedOutliers | Simulated Outliers |
| subsetExons | Extract first/last exons depending on strand takes the first... |
| summarise_counts | convenience function that adds summary statistics to given... |
| tssRegions | Transcription start site regions |
| unnest_dt | Flatten data.tables with list entries |
| writeResults | Select columns and write to tsv file |
