seqsetvis

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7

Set Based Visualizations for Next-Gen Sequencing Data

Bioconductor version: Development (3.24)

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: 0000-0002-8969-9676

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

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

Joseph R Boyd. seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data. doi:10.18129/B9.bioc.seqsetvis, R package version 1.33.3, https://bioconductor.org/packages/seqsetvis.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ChIPSeq, MultipleComparison, Sequencing, Software, Visualization
Version	1.33.3
In Bioconductor since	BioC 3.7 (R-3.5) (8.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.3), ggplot2
Imports	cowplot, data.table, eulerr, Seqinfo, GenomeInfoDb, GenomicAlignments, GenomicRanges, ggplotify, grDevices, grid, IRanges, limma, methods, pbapply, pbmcapply, png, RColorBrewer, Rsamtools, rtracklayer, S4Vectors, scales, stats, UpSetR
System Requirements
URL

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, r-universe

Package Archives

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

Source Package	seqsetvis_1.33.3.tar.gz
Windows Binary (x86_64)	seqsetvis_1.33.3.zip (64-bit only)
macOS Binary (big-sur-x86_64)	seqsetvis_1.33.3.tgz
macOS Binary (sonoma-arm64)	seqsetvis_1.33.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/seqsetvis
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/seqsetvis
Package Short Url	https://bioconductor.org/packages/seqsetvis/
Package Downloads Report	Download Stats