trackViewer
This is the development version of trackViewer; for the stable release version, see 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: Development (3.21)
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.
Author: Jianhong Ou [aut, cre] (ORCID:
Maintainer: Jianhong Ou <jianhong.ou at duke.edu>
citation("trackViewer")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("trackViewer")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("trackViewer")| trackViewer Vignette: change the track styles | HTML | R Script |
| trackViewer Vignette: dandelionPlot | HTML | R Script |
| trackViewer Vignette: lollipopPlot | HTML | R Script |
| trackViewer Vignette: overview | HTML | R Script |
| trackViewer Vignette: plot interaction data | HTML | R Script |
| Reference Manual |
Details
| biocViews | Software, Visualization |
| Version | 1.43.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (10.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.5.0), grDevices, methods, GenomicRanges, grid |
| Imports | GenomeInfoDb, GenomicAlignments, GenomicFeatures, Gviz, Rsamtools, S4Vectors, rtracklayer, BiocGenerics, scales, tools, IRanges, AnnotationDbi, grImport, htmlwidgets, InteractionSet, utils, rhdf5, strawr, txdbmaker |
| System Requirements | |
| URL |
See More
| Suggests | biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr, htmltools, rmarkdown, motifStack |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | NADfinder, geomeTriD |
| Suggests Me | ATACseqQC, ChIPpeakAnno |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | trackViewer_1.43.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/trackViewer |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/trackViewer |
| Bioc Package Browser | https://code.bioconductor.org/browse/trackViewer/ |
| Package Short Url | https://bioconductor.org/packages/trackViewer/ |
| Package Downloads Report | Download Stats |