seqsetvis
This is thereleased version of seqsetvis; for the devel version, seeseqsetvis.
Set Based Visualizations for Next-Gen Sequencing Data
Bioconductor version: Release (3.22)
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("seqsetvis")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("seqsetvis")For older versions of R, please refer to the appropriateBioconductor 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 | 1.30.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (7.5 years) |
| License | MIT + fileLICENSE |
| Depends | R (>= 4.3),ggplot2 |
| Imports | cowplot,data.table,eulerr,Seqinfo,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,GenomeInfoDb,covr,knitr,rmarkdown,testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | seqsetvis_1.30.0.tar.gz |
| Windows Binary (x86_64) | seqsetvis_1.30.0.zip |
| macOS Binary (x86_64) | seqsetvis_1.30.0.tgz |
| macOS Binary (arm64) | seqsetvis_1.30.0.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 |