seqsetvis

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see seqsetvis.

Set Based Visualizations for Next-Gen Sequencing Data

Bioconductor version: 3.8

seqsetvis enables the visualization and analysis of multiple genomic datasets. Although seqsetvis was designed for the comparison of mulitple ChIP-seq datasets, this package is domain-agnostic and allows the processing of multiple genomic coordinate files (bed-like files) and signal files (bigwig files or bam pileups).

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 "3.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ChIPSeq, Sequencing, Software, Visualization

Version 1.2.1

In Bioconductor since BioC 3.7 (R-3.5) (6 years)

License MIT + file LICENSE

Depends R (>= 3.5), ggplot2

Imports data.table, eulerr, GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices, grid, IRanges, limma, methods, png, RColorBrewer, Rsamtools, rtracklayer, S4Vectors, stats

System Requirements

URL

Suggests BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr, cowplot, 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_1.2.1.tar.gz

Windows Binary seqsetvis_1.2.1.zip

Mac OS X 10.11 (El Capitan) seqsetvis_1.2.1.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

Old Source Packages for BioC 3.8 Source Archive