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Bioconductor - GenomicPlot (development version)

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 (3.22)

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] ORCID: 0000-0002-6664-8438

Maintainer: Shuye Pu <shuye2009 at gmail.com>

Citation (from within R, enter citation("GenomicPlot")): 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("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")
Details biocViews AlternativeSplicing, Annotation, ChIPSeq, Coverage, GeneExpression, RNASeq, Sequencing, Software, Transcription, Visualization Version 1.7.1 In Bioconductor since BioC 3.18 (R-4.3) (1.5 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, 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(>= 1.36.0), 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 Package Archives

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

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