trackViewer
A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data
Bioconductor version: 3.23 · Package version: 1.48.0
Visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("trackViewer") Details
| Maintainer | Jianhong Ou <jou@morgridge.org> |
| Author | Jianhong Ou [aut, cre] (ORCID: <https://orcid.org/0000-0002-8652-2488>), Julie Lihua Zhu [aut] |
| License | GPL (>= 2) |
| Downloads rank | 1043 |
| Source branch | RELEASE_3_23 |
| biocViews | Software, Visualization |
Documentation
- trackViewer Vignette: change the track styles
- trackViewer Vignette: dandelionPlot
- trackViewer Vignette: lollipopPlot
- trackViewer Vignette: overview
- trackViewer Vignette: plot interaction data
Download
Dependencies
Depends: R (>= 3.5.0), grDevices, methods, GenomicRanges, grid
Imports: Seqinfo, GenomeInfoDb, GenomicAlignments, GenomicFeatures, Gviz, Rsamtools, S4Vectors, rtracklayer, BiocGenerics, scales, tools, IRanges, AnnotationDbi, grImport, htmlwidgets, InteractionSet, utils, rhdf5, strawr, txdbmaker
Suggests: biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr, htmltools, rmarkdown, motifStack
Reverse dependencies
Imports Me (3): annoLinker, geomeTriD, NADfinder
Suggests Me (3): ATACseqQC, ChIPpeakAnno, MutSeqR