seqsetvis

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

Set Based Visualizations for Next-Gen Sequencing Data


Bioconductor version: Development (3.21)

seqsetvis enables the visualization and analysis of sets of genomic sites in next gen sequencing data. Although seqsetvis was designed for the comparison of mulitple ChIP-seq samples, this package is domain-agnostic and allows the processing of multiple genomic coordinate files (bed-like files) and signal files (bigwig files pileups from bam file). seqsetvis has multiple functions for fetching data from regions into a tidy format for analysis in data.table or tidyverse and visualization via ggplot2.

Author: Joseph R Boyd [aut, cre] (ORCID: )

Maintainer: Joseph R Boyd <jrboyd at uvm.edu>

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

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("seqsetvis")

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("seqsetvis")
Overview and Use Cases HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews ChIPSeq, MultipleComparison, Sequencing, Software, Visualization
Version 1.27.0
In Bioconductor since BioC 3.7 (R-3.5) (6.5 years)
License MIT + file LICENSE
Depends R (>= 4.3), ggplot2
Imports cowplot, data.table, eulerr, GenomeInfoDb, GenomicAlignments, GenomicRanges, ggplotify, grDevices, grid, IRanges, limma, methods, pbapply, pbmcapply, png, RColorBrewer, Rsamtools, rtracklayer, S4Vectors, scales, stats, UpSetR
System Requirements
URL
See More
Suggests BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr, knitr, rmarkdown, testthat
Linking To
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Depends On Me
Imports Me
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Package Archives

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

Source Package seqsetvis_1.27.0.tar.gz
Windows Binary (x86_64) seqsetvis_1.27.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/seqsetvis
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/seqsetvis
Bioc Package Browser https://code.bioconductor.org/browse/seqsetvis/
Package Short Url https://bioconductor.org/packages/seqsetvis/
Package Downloads Report Download Stats