seqsetvis

DOI: 10.18129/B9.bioc.seqsetvis    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see seqsetvis.

Set Based Visualizations for Next-Gen Sequencing Data

Bioconductor version: 3.13

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	Overview and Use Cases
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	ChIPSeq, MultipleComparison, Sequencing, Software, Visualization
Version	1.12.0
In Bioconductor since	BioC 3.7 (R-3.5) (3.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.6), ggplot2
Imports	data.table, eulerr, GenomeInfoDb, GenomicAlignments, GenomicRanges, ggplotify, grDevices, grid, IRanges, limma, methods, pbapply, pbmcapply, png, RColorBrewer, Rsamtools, rtracklayer, S4Vectors, stats, UpSetR
LinkingTo
Suggests	BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr, cowplot, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	seqsetvis_1.12.0.tar.gz
Windows Binary	seqsetvis_1.12.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	seqsetvis_1.12.0.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