Man pages for paul-shannon/igvShiny
igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive tool for visualization and exploration integrated genomic data)
| display | display the already constructed and configured track |
| get_basic_genomes | get_basic_genomes |
| get_cas_genomes | get_cas_genomes |
| get_css_genomes | get_css_genomes |
| get_tracks_dir | get_tracks_dir Get the directory where tracks are stored. The... |
| getUrl | the url of the gwas table |
| GWASTrack-class | Constructor for GWASTrack |
| igvShiny | Create an igvShiny instance |
| igvShinyOutput | create the UI for the widget |
| loadBamTrackFromLocalData | load GenomicAlignments data as an igv.js alignment track |
| loadBamTrackFromURL | load a bam track which, with index, is served up by http |
| loadBedGraphTrackFromURL | load a bedgraph track from a URL |
| loadBedTrack | load a bed track provided as a data.frame |
| loadCramTrackFromURL | load a cram track which, with index, is served up by http |
| loadGenomeAnnotationTrack | load a scored genome annotation track provided as a... |
| loadGFF3TrackFromLocalData | load a GFF3 track defined by local data |
| loadGFF3TrackFromURL | load a GFF3 track which, with index, is served up by http |
| loadGwasTrack | load a GWAS (genome-wide association study) track provided as... |
| loadSEGTrack | load a seg track provided as a data.frame |
| loadVcfTrack | load a VCF (variant) track provided as a Bioconductor... |
| parseAndValidateGenomeSpec | parseAndValidateGenomeSpec |
| removeTracksByName | remove tracks from the browser |
| removeUserAddedTracks | remove only those tracks explicitly added by your app |
| renderIgvShiny | draw the igv genome browser element |
| showGenomicRegion | focus igv on a region |
