trackViewer
This is the released version of trackViewer; for the devel 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: Release (3.23)
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]
, Julie Lihua Zhu [aut]
Maintainer: Jianhong Ou <jou at morgridge.org>
citation("trackViewer")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
| NEWS | Text |
Details
| biocViews | Software, Visualization |
| Version | 1.48.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (12.5 years) |
| License | GPL (>= 2) |
| 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 |
| 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 | annoLinker, geomeTriD, NADfinder |
| Suggests Me | ATACseqQC, ChIPpeakAnno, MutSeqR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | trackViewer_1.48.0.tar.gz |
| Windows Binary (x86_64) | trackViewer_1.48.0.zip |
| macOS Binary (big-sur-x86_64) | trackViewer_1.48.0.tgz |
| macOS Binary (sonoma-arm64) | trackViewer_1.48.0.tgz |
| 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 |