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seqsetvis

Set Based Visualizations for Next-Gen Sequencing Data


Bioconductor version: Release (3.19)

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).

Author: Joseph R Boyd [aut, cre]

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

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

Installation

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


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

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 1.24.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License MIT + file LICENSE
Depends R (>= 3.6), 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
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package seqsetvis_1.24.0.tar.gz
Windows Binary seqsetvis_1.24.0.zip
macOS Binary (x86_64) seqsetvis_1.24.0.tgz
macOS Binary (arm64) seqsetvis_1.24.0.tgz
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