seqplots (version 1.10.2)
An interactive tool for visualizing NGS signals and sequence
motif densities along genomic features using average plots and heatmaps
Description
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.