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Bioconductor - plotgardener (development version)

plotgardener

This is the development version of plotgardener; for the stable release version, see plotgardener.

Coordinate-Based Genomic Visualization Package for R

Bioconductor version: Development (3.22)

Coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots are placed and arranged on a page.

Author: Nicole Kramer [aut, cre], Eric S. Davis [aut], Craig Wenger [aut], Sarah Parker [ctb], Erika Deoudes [art], Michael Love [ctb], Douglas H. Phanstiel [aut, cre, cph]

Maintainer: Nicole Kramer <nekramer27 at gmail.com>, Douglas Phanstiel <douglas_phanstiel at med.unc.edu>

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

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("plotgardener")
Details biocViews FunctionalGenomics, GenomeAnnotation, GenomeAssembly, HiC, Software, Visualization Version 1.15.1 In Bioconductor since BioC 3.14 (R-4.1) (3.5 years) License MIT + file LICENSE Depends R (>= 4.2.0) Imports curl, data.table, dplyr, GenomeInfoDb, GenomicRanges, glue, grDevices, grid, ggplotify, IRanges, methods, plyranges, purrr, Rcpp, RColorBrewer, rhdf5, rlang, stats, strawr, tools, utils, withr System Requirements URL https://phanstiellab.github.io/plotgardener https://github.com/PhanstielLab/plotgardener Bug Reports https://github.com/PhanstielLab/plotgardener/issues See More Suggests AnnotationDbi, AnnotationHub, BSgenome, BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, GenomicFeatures, ggplot2, InteractionSet, knitr, org.Hs.eg.db, rtracklayer, plotgardenerData, pdftools, png, rmarkdown, scales, showtext, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene Linking To Rcpp Enhances Depends On Me Imports Me DegCre, mariner, Ularcirc Suggests Me nullranges, rigvf Links To Me Build Report Build Report Package Archives

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

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