the path to data directory, it will be created if not existing

root

run the SeqPlots in debug mode, i.e. with R console embedded in 
web interface

debug

arguments sent to <code><a href="/link/runApp?package=seqplots&version=1.10.2&to=shiny" rd-options="shiny" data-mini-rdoc="shiny::runApp">runApp</a></code> function

This function initaite SeqPlots and oppens 
web browser with graphical user interface (GUI).

seqplots

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.

Przemyslaw Stempor

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

run function

arguments sent to <code><a href="runApp" rd-options="shiny">runApp</a></code> function

run: SeqPlots innitiation

Description

Usage

Arguments

Value

Details

Examples