Package: seqplots
Maintainer: Przemyslaw Stempor <ps562@cam.ac.uk>
Author: Przemyslaw Stempor
Version: 1.12.0
License: GPL-3
Title: 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.
URL: http://github.com/przemol/seqplots
BugReports: http://github.com/przemol/seqplots/issues
biocViews: ChIPSeq, RNASeq, Sequencing, Software, Visualization
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
Type: Package
Date: 2014-09-15
LazyLoad: yes
VignetteBuilder: knitr
Suggests: testthat, BiocStyle, knitr, rmarkdown
Collate: 'MotifSetup-class.R' 'PlotSetPair-class.R'
        'PlotSetArray-class.R' 'PlotSetList-class.R'
        'deployServerInstance.R' 'generic_methods.R'
        'getPlotSetArray.R' 'helper_functions.R' 'int_getSF.R'
        'int_ggHeatmapPlotWrapper.R' 'int_heatmapPlotWrapper.R'
        'int_imPlot2.R' 'int_plotMext.R' 'plotAverage.R'
        'plotHeatmap.R' 'run.R' 'seqplots-package.R' 'zzz.R'
RoxygenNote: 5.0.1
Remotes: github::rstudio/DT
NeedsCompilation: no
Packaged: 2016-10-18 00:02:04 UTC; biocbuild
Built: R 3.3.1; ; 2016-10-18 04:43:22 UTC; windows
