seqplots

DOI: 10.18129/B9.bioc.seqplots    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see seqplots.

An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps

Bioconductor version: 3.10

SeqPlots is a tool for plotting next generation sequencing (NGS) based experiments' signal tracks, e.g. reads coverage from ChIP-seq, RNA-seq and DNA accessibility assays like DNase-seq and MNase-seq, over user specified genomic features, e.g. promoters, gene bodies, etc. It can also calculate sequence motif density profiles from reference genome. The data are visualized as average signal profile plot, with error estimates (standard error and 95% confidence interval) shown as fields, or as series of heatmaps that can be sorted and clustered using hierarchical clustering, k-means algorithm and self organising maps. Plots can be prepared using R programming language or web browser based graphical user interface (GUI) implemented using Shiny framework. The dual-purpose implementation allows running the software locally on desktop or deploying it on server. SeqPlots is useful for both for exploratory data analyses and preparing replicable, publication quality plots. Other features of the software include collaboration and data sharing capabilities, as well as ability to store pre-calculated result matrixes, that combine many sequencing experiments and in-silico generated tracks with multiple different features. These binaries can be further used to generate new combination plots on fly, run automated batch operations or share with colleagues, who can adjust their plotting parameters without loading actual tracks and recalculating numeric values. SeqPlots relays on Bioconductor packages, mainly on rtracklayer for data input and BSgenome packages for reference genome sequence and annotations.

Author: Przemyslaw Stempor [aut, cph, cre]

Maintainer: Przemyslaw Stempor <ps562 at cam.ac.uk>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("seqplots")

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("seqplots")

 

HTML	R Script	SeqPlots GUI
HTML	R Script	SeqPlots Quick Start
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, ImmunoOncology, RNASeq, Sequencing, Software, Visualization
Version	1.24.0
In Bioconductor since	BioC 3.0 (R-3.1) (5.5 years)
License	GPL-3
Depends	R (>= 3.2.0)
Imports	methods, IRanges, BSgenome, digest, rtracklayer, GenomicRanges, Biostrings, shiny (>= 0.13.0), DBI, RSQLite, plotrix, fields, grid, kohonen, parallel, GenomeInfoDb, class, S4Vectors, ggplot2, reshape2, gridExtra, jsonlite, DT (>= 0.1.0), RColorBrewer, Rsamtools, GenomicAlignments, BiocManager
LinkingTo
Suggests	testthat, BiocStyle, knitr, rmarkdown, covr
SystemRequirements
Enhances
URL	http://github.com/przemol/seqplots
BugReports	http://github.com/przemol/seqplots/issues
Depends On Me
Imports Me	ChIPSeqSpike
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	seqplots_1.24.0.tar.gz
Windows Binary	seqplots_1.24.0.zip
Mac OS X 10.11 (El Capitan)	seqplots_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/seqplots
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/seqplots
Package Short Url	https://bioconductor.org/packages/seqplots/
Package Downloads Report	Download Stats