GenomicPlot
This is the development version of GenomicPlot; for the stable release version, see GenomicPlot.
Plot profiles of next generation sequencing data in genomic features
Bioconductor version: Development (3.24)
Visualization of next generation sequencing (NGS) data is essential for interpreting high-throughput genomics experiment results. 'GenomicPlot' facilitates plotting of NGS data in various formats (bam, bed, wig and bigwig); both coverage and enrichment over input can be computed and displayed with respect to genomic features (such as UTR, CDS, enhancer), and user defined genomic loci or regions. Statistical tests on signal intensity within user defined regions of interest can be performed and represented as boxplots or bar graphs. Parallel processing is used to speed up computation on multicore platforms. In addition to genomic plots which is suitable for displaying of coverage of genomic DNA (such as ChIPseq data), metagenomic (without introns) plots can also be made for RNAseq or CLIPseq data as well.
Author: Shuye Pu <shuye2009 at gmail.com>
Maintainer: Shuye Pu <shuye2009 at gmail.com>
citation("GenomicPlot")):Shuye Pu. GenomicPlot: Plot profiles of next generation sequencing data in genomic features. doi:10.18129/B9.bioc.GenomicPlot, R package version 1.11.0, https://bioconductor.org/packages/GenomicPlot.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("GenomicPlot")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("GenomicPlot")| GenomicPlot_vignettes.html | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | AlternativeSplicing, Annotation, ChIPSeq, Coverage, GeneExpression, RNASeq, Sequencing, Software, Transcription, Visualization |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 years) |
| License | GPL-2 |
| Depends | R (>= 4.4.0), GenomicRanges (>= 1.46.1) |
| Imports | methods, Rsamtools, parallel, tidyr, rtracklayer (>= 1.54.0), plyranges (>= 1.14.0), cowplot (>= 1.1.1), VennDiagram, ggplotify, Seqinfo, IRanges, ComplexHeatmap, RCAS (>= 1.20.0), scales (>= 1.2.0), GenomicAlignments (>= 1.30.0), edgeR, circlize, viridis, ggsignif (>= 0.6.3), ggsci (>= 2.9), ggpubr, grDevices, graphics, stats, utils, GenomicFeatures, genomation (>= 1.36.0), txdbmaker, ggplot2 (>= 3.3.5), BiocGenerics, dplyr, grid, GenomeInfoDb |
| System Requirements | |
| URL | https://github.com/shuye2009/GenomicPlot |
| Bug Reports | https://github.com/shuye2009/GenomicPlot/issues |
See More
| Suggests | knitr, rmarkdown, R.utils, Biobase, BiocStyle, testthat, AnnotationDbi |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GenomicPlot_1.11.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | GenomicPlot_1.11.0.tgz |
| macOS Binary (sonoma-arm64) | GenomicPlot_1.11.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GenomicPlot |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GenomicPlot |
| Package Short Url | https://bioconductor.org/packages/GenomicPlot/ |
| Package Downloads Report | Download Stats |