A B C D E F G H I K L M N O P R S T U V W misc
| addScheme | Setting display parameters to control the look and feel of the plots |
| AlignedReadTrack | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE) |
| AlignedReadTrack-class | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE) |
| AlignmentsTrack | AlignmentsTrack class and methods |
| AlignmentsTrack-class | AlignmentsTrack class and methods |
| AnnotationTrack | AnnotationTrack class and methods |
| AnnotationTrack-class | AnnotationTrack class and methods |
| as.list-method | DisplayPars class and method |
| availableDefaultMapping | ReferenceTrack class and methods |
| availableDisplayPars | DisplayPars class and method |
| axTrack | Data sets |
| BiomartGeneRegionTrack | BiomartGeneRegionTrack class and methods |
| BiomartGeneRegionTrack-class | BiomartGeneRegionTrack class and methods |
| biomTrack | Data sets |
| bmt | Data sets |
| bmTrack | Data sets |
| chromosome | RangeTrack class and methods |
| chromosome-method | GdObject class and methods |
| chromosome-method | RangeTrack class and methods |
| chromosome-method | SequenceTrack class and methods |
| chromosome<- | RangeTrack class and methods |
| chromosome<--method | AlignmentsTrack class and methods |
| chromosome<--method | GdObject class and methods |
| chromosome<--method | HighlightTrack class and methods |
| chromosome<--method | IdeogramTrack class and methods |
| chromosome<--method | OverlayTrack class and methods |
| chromosome<--method | RangeTrack class and methods |
| chromosome<--method | SequenceTrack class and methods |
| clearSessionCache | Meta-constructor for GenomeGraph tracks fetched directly from the various UCSC data sources. |
| coerce-method | AnnotationTrack class and methods |
| coerce-method | DataTrack class and methods |
| coerce-method | DisplayPars class and method |
| coerce-method | GeneRegionTrack class and methods |
| coerce-method | RangeTrack class and methods |
| coerce-method | SequenceTrack class and methods |
| collapseTrack-method | AnnotationTrack class and methods |
| collapseTrack-method | DataTrack class and methods |
| collapseTrack-method | GeneRegionTrack class and methods |
| collapseTrack-method | GenomeAxisTrack class and methods |
| collapsing | Dynamic content based on the available resolution |
| conservation | Data sets |
| consolidateTrack | GdObject class and methods |
| consolidateTrack-method | AnnotationTrack class and methods |
| consolidateTrack-method | GdObject class and methods |
| consolidateTrack-method | HighlightTrack class and methods |
| consolidateTrack-method | OverlayTrack class and methods |
| consolidateTrack-method | RangeTrack class and methods |
| consolidateTrack-method | SequenceTrack class and methods |
| consolidateTrack-method | StackedTrack class and methods |
| coords | GdObject class and methods |
| coords-method | GdObject class and methods |
| coords-method | ImageMap class and methods |
| coverage-method | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE) |
| coverage-method | AlignmentsTrack class and methods |
| cpgIslands | Data sets |
| ctrack | Data sets |
| CustomTrack | CustomTrack class and methods |
| CustomTrack-class | CustomTrack class and methods |
| cyp2b10 | Data sets |
| DataTrack | DataTrack class and methods |
| DataTrack-class | DataTrack class and methods |
| denseAnnTrack | Data sets |
| DetailsAnnotationTrack | AnnotationTrack class and methods |
| DetailsAnnotationTrack-class | AnnotationTrack class and methods |
| DisplayPars | DisplayPars class and method |
| displayPars | DisplayPars class and method |
| DisplayPars-class | DisplayPars class and method |
| displayPars-method | DisplayPars class and method |
| displayPars-method | GdObject class and methods |
| displayPars<- | DisplayPars class and method |
| displayPars<--method | DisplayPars class and method |
| displayPars<--method | GdObject class and methods |
| displayPars<--method | HighlightTrack class and methods |
| displayPars<--method | OverlayTrack class and methods |
| drawAxis | GdObject class and methods |
| drawAxis-method | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE) |
| drawAxis-method | AlignmentsTrack class and methods |
| drawAxis-method | DataTrack class and methods |
| drawAxis-method | GdObject class and methods |
| drawAxis-method | NumericTrack class and methods |
| drawGD | GdObject class and methods |
| drawGD-method | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE) |
| drawGD-method | AlignmentsTrack class and methods |
| drawGD-method | AnnotationTrack class and methods |
| drawGD-method | CustomTrack class and methods |
| drawGD-method | DataTrack class and methods |
| drawGD-method | GdObject class and methods |
| drawGD-method | GenomeAxisTrack class and methods |
| drawGD-method | IdeogramTrack class and methods |
| drawGD-method | OverlayTrack class and methods |
| drawGD-method | StackedTrack class and methods |
| drawGrid-method | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE) |
| drawGrid-method | AnnotationTrack class and methods |
| drawGrid-method | GdObject class and methods |
| drawGrid-method | NumericTrack class and methods |
| dtHoriz | Data sets |
| end-method | GenomeAxisTrack class and methods |
| end-method | IdeogramTrack class and methods |
| end-method | RangeTrack class and methods |
| end-method | SequenceTrack class and methods |
| end<--method | GenomeAxisTrack class and methods |
| end<--method | IdeogramTrack class and methods |
| end<--method | RangeTrack class and methods |
| ensGenes | Data sets |
| exon | GeneRegionTrack class and methods |
| exon-method | GeneRegionTrack class and methods |
| exon<- | GeneRegionTrack class and methods |
| exon<--method | GeneRegionTrack class and methods |
| exportTracks | Export GenomeGraph tracks to a annotation file representation. |
| feature | RangeTrack class and methods |
| feature-method | DataTrack class and methods |
| feature-method | RangeTrack class and methods |
| feature<- | RangeTrack class and methods |
| feature<--method | DataTrack class and methods |
| feature<--method | RangeTrack class and methods |
| from | Data sets |
| gcContent | Data sets |
| GdObject | GdObject class and methods |
| GdObject-class | GdObject class and methods |
| gene | GeneRegionTrack class and methods |
| gene-method | GeneRegionTrack class and methods |
| gene<- | GeneRegionTrack class and methods |
| gene<--method | GeneRegionTrack class and methods |
| geneDetails | Data sets |
| geneModels | Data sets |
| GeneRegionTrack | GeneRegionTrack class and methods |
| GeneRegionTrack-class | GeneRegionTrack class and methods |
| genome-method | RangeTrack class and methods |
| genome-method | SequenceTrack class and methods |
| genome<--method | GdObject class and methods |
| genome<--method | IdeogramTrack class and methods |
| genome<--method | RangeTrack class and methods |
| GenomeAxisTrack | GenomeAxisTrack class and methods |
| GenomeAxisTrack-class | GenomeAxisTrack class and methods |
| getPar | DisplayPars class and method |
| getPar-method | DisplayPars class and method |
| getPar-method | GdObject class and methods |
| getScheme | Setting display parameters to control the look and feel of the plots |
| group | AnnotationTrack class and methods |
| group-method | AnnotationTrack class and methods |
| group-method | GdObject class and methods |
| group-method | GeneRegionTrack class and methods |
| group<- | AnnotationTrack class and methods |
| group<--method | AnnotationTrack class and methods |
| group<--method | GeneRegionTrack class and methods |
| grouping | Grouping of annotation features |
| head-method | DisplayPars class and method |
| HighlightTrack | HighlightTrack class and methods |
| HighlightTrack-class | HighlightTrack class and methods |
| identifier | AnnotationTrack class and methods |
| identifier-method | AnnotationTrack class and methods |
| identifier-method | GeneRegionTrack class and methods |
| identifier<- | AnnotationTrack class and methods |
| identifier<--method | AnnotationTrack class and methods |
| identifier<--method | GeneRegionTrack class and methods |
| IdeogramTrack | IdeogramTrack class and methods |
| IdeogramTrack-class | IdeogramTrack class and methods |
| ideoTrack | Data sets |
| idTrack | Data sets |
| idxTrack | Data sets |
| imageMap | GdObject class and methods |
| ImageMap-class | ImageMap class and methods |
| imageMap-method | GdObject class and methods |
| initialize-method | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE) |
| initialize-method | AlignmentsTrack class and methods |
| initialize-method | AnnotationTrack class and methods |
| initialize-method | BiomartGeneRegionTrack class and methods |
| initialize-method | CustomTrack class and methods |
| initialize-method | DataTrack class and methods |
| initialize-method | DisplayPars class and method |
| initialize-method | GdObject class and methods |
| initialize-method | GeneRegionTrack class and methods |
| initialize-method | GenomeAxisTrack class and methods |
| initialize-method | HighlightTrack class and methods |
| initialize-method | IdeogramTrack class and methods |
| initialize-method | OverlayTrack class and methods |
| initialize-method | RangeTrack class and methods |
| initialize-method | ReferenceTrack class and methods |
| initialize-method | SequenceTrack class and methods |
| initialize-method | StackedTrack class and methods |
| isActiveSeq-method | RangeTrack class and methods |
| isActiveSeq<--method | GdObject class and methods |
| itrack | Data sets |
| knownGenes | Data sets |
| length-method | GenomeAxisTrack class and methods |
| length-method | HighlightTrack class and methods |
| length-method | IdeogramTrack class and methods |
| length-method | OverlayTrack class and methods |
| length-method | RangeTrack class and methods |
| length-method | SequenceTrack class and methods |
| max-method | RangeTrack class and methods |
| min-method | RangeTrack class and methods |
| names-method | GdObject class and methods |
| names<--method | GdObject class and methods |
| NumericTrack | NumericTrack class and methods |
| NumericTrack-class | NumericTrack class and methods |
| OverlayTrack | OverlayTrack class and methods |
| OverlayTrack-class | OverlayTrack class and methods |
| plotTracks | The main plotting function for one or several GenomeGraph tracks. |
| position | RangeTrack class and methods |
| position-method | IdeogramTrack class and methods |
| position-method | RangeTrack class and methods |
| range | RangeTrack class and methods |
| range-method | DataTrack class and methods |
| range-method | GenomeAxisTrack class and methods |
| range-method | RangeTrack class and methods |
| ranges-method | GenomeAxisTrack class and methods |
| ranges-method | RangeTrack class and methods |
| ranges<--method | GenomeAxisTrack class and methods |
| ranges<--method | RangeTrack class and methods |
| RangeTrack | RangeTrack class and methods |
| RangeTrack-class | RangeTrack class and methods |
| ReferenceTrack | ReferenceTrack class and methods |
| ReferenceTrack-class | ReferenceTrack class and methods |
| refGenes | Data sets |
| score-method | DataTrack class and methods |
| seqinfo-method | RangeTrack class and methods |
| seqlevels-method | RangeTrack class and methods |
| seqlevels-method | SequenceTrack class and methods |
| seqnames-method | RangeTrack class and methods |
| seqnames-method | SequenceTrack class and methods |
| SequenceTrack | SequenceTrack class and methods |
| SequenceTrack-class | SequenceTrack class and methods |
| setCoverage-method | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE) |
| setPar | DisplayPars class and method |
| setPar-method | DisplayPars class and method |
| setPar-method | GdObject class and methods |
| setStacks-method | AnnotationTrack class and methods |
| setStacks-method | HighlightTrack class and methods |
| setStacks-method | OverlayTrack class and methods |
| setStacks-method | StackedTrack class and methods |
| settings | Setting display parameters to control the look and feel of the plots |
| show-method | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE) |
| show-method | AlignmentsTrack class and methods |
| show-method | AnnotationTrack class and methods |
| show-method | CustomTrack class and methods |
| show-method | DataTrack class and methods |
| show-method | DisplayPars class and method |
| show-method | GeneRegionTrack class and methods |
| show-method | GenomeAxisTrack class and methods |
| show-method | HighlightTrack class and methods |
| show-method | IdeogramTrack class and methods |
| show-method | OverlayTrack class and methods |
| snpLocations | Data sets |
| split-method | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE) |
| split-method | DataTrack class and methods |
| split-method | RangeTrack class and methods |
| StackedTrack | StackedTrack class and methods |
| StackedTrack-class | StackedTrack class and methods |
| stacking | StackedTrack class and methods |
| stacking-method | StackedTrack class and methods |
| stacking<- | StackedTrack class and methods |
| stacking<--method | StackedTrack class and methods |
| stacks | StackedTrack class and methods |
| stacks-method | AlignmentsTrack class and methods |
| stacks-method | StackedTrack class and methods |
| start-method | GenomeAxisTrack class and methods |
| start-method | IdeogramTrack class and methods |
| start-method | RangeTrack class and methods |
| start-method | SequenceTrack class and methods |
| start<--method | GenomeAxisTrack class and methods |
| start<--method | IdeogramTrack class and methods |
| start<--method | RangeTrack class and methods |
| strand-method | DataTrack class and methods |
| strand-method | GenomeAxisTrack class and methods |
| strand-method | RangeTrack class and methods |
| strand<--method | DataTrack class and methods |
| strand<--method | RangeTrack class and methods |
| subseq-method | SequenceTrack class and methods |
| subset-method | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE) |
| subset-method | AlignmentsTrack class and methods |
| subset-method | AnnotationTrack class and methods |
| subset-method | BiomartGeneRegionTrack class and methods |
| subset-method | DataTrack class and methods |
| subset-method | GdObject class and methods |
| subset-method | GeneRegionTrack class and methods |
| subset-method | GenomeAxisTrack class and methods |
| subset-method | HighlightTrack class and methods |
| subset-method | IdeogramTrack class and methods |
| subset-method | OverlayTrack class and methods |
| subset-method | RangeTrack class and methods |
| subset-method | StackedTrack class and methods |
| symbol | GeneRegionTrack class and methods |
| symbol-method | GeneRegionTrack class and methods |
| symbol<- | GeneRegionTrack class and methods |
| symbol<--method | GeneRegionTrack class and methods |
| tags | GdObject class and methods |
| tags-method | GdObject class and methods |
| tags-method | ImageMap class and methods |
| tail-method | DisplayPars class and method |
| to | Data sets |
| transcript | GeneRegionTrack class and methods |
| transcript-method | GeneRegionTrack class and methods |
| transcript<- | GeneRegionTrack class and methods |
| transcript<--method | GeneRegionTrack class and methods |
| twoGroups | Data sets |
| UcscTrack | Meta-constructor for GenomeGraph tracks fetched directly from the various UCSC data sources. |
| values-method | AlignmentsTrack class and methods |
| values-method | DataTrack class and methods |
| values-method | GenomeAxisTrack class and methods |
| values-method | RangeTrack class and methods |
| values<--method | DataTrack class and methods |
| width-method | GenomeAxisTrack class and methods |
| width-method | IdeogramTrack class and methods |
| width-method | RangeTrack class and methods |
| width-method | SequenceTrack class and methods |
| width<--method | IdeogramTrack class and methods |
| width<--method | RangeTrack class and methods |
| [ | RangeTrack class and methods |
| [-method | AlignedReadTrack class and methods (NOTE: THIS IS STILL IN DEVELOPMENT AND SUBJECT TO CHANGE) |
| [-method | AlignmentsTrack class and methods |
| [-method | DataTrack class and methods |
| [-method | GenomeAxisTrack class and methods |
| [-method | IdeogramTrack class and methods |
| [-method | RangeTrack class and methods |
| [-method | StackedTrack class and methods |