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("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 | ||
| 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 | |
| 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_1.27.0.tar.gz |
| Windows Binary (x86_64) | seqsetvis_1.27.0.zip (64-bit only) |
| 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 |