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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 (3.19)

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 [aut, cre]

Maintainer: Shuye Pu <shuye2009 at gmail.com>

Citation (from within R, enter citation("GenomicPlot")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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 PDF
NEWS Text

Details

biocViews AlternativeSplicing, Annotation, ChIPSeq, Coverage, GeneExpression, RNASeq, Sequencing, Software, Transcription, Visualization
Version 1.1.8
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License GPL-2
Depends R (>= 4.3.0), GenomicRanges(>= 1.46.1)
Imports methods, Rsamtools, parallel, tidyr, rtracklayer(>= 1.54.0), plyranges(>= 1.14.0), cowplot (>= 1.1.1), VennDiagram, ggplotify, GenomeInfoDb, 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(>= 1.26.0), txdbmaker, ggplot2 (>= 3.3.5), BiocGenerics, dplyr, grid
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
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package GenomicPlot_1.1.8.tar.gz
Windows Binary GenomicPlot_1.1.8.zip
macOS Binary (x86_64) GenomicPlot_1.1.8.tgz
macOS Binary (arm64) GenomicPlot_1.1.8.tgz
Source Repository git clone https://git.bioconductor.org/packages/GenomicPlot
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GenomicPlot
Bioc Package Browser https://code.bioconductor.org/browse/GenomicPlot/
Package Short Url https://bioconductor.org/packages/GenomicPlot/
Package Downloads Report Download Stats