Type: Package
Package: seqplots
Title: An interactive tool for visualizing NGS signals and sequence
        motif densities along genomic features using average plots and
        heatmaps
Version: 1.22.2
Date: 2014-09-15
Authors@R: 
    person(given = "Przemyslaw",
           family = "Stempor",
           role = c("aut", "cph", "cre"),
           email = "ps562@cam.ac.uk")
Maintainer: Przemyslaw Stempor <ps562@cam.ac.uk>
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.
License: GPL-3
URL: http://github.com/przemol/seqplots
BugReports: http://github.com/przemol/seqplots/issues
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
Suggests: testthat, BiocStyle, knitr, rmarkdown, covr
VignetteBuilder: knitr
biocViews: ImmunoOncology, ChIPSeq, RNASeq, Sequencing, Software,
        Visualization
LazyLoad: yes
RoxygenNote: 6.1.1
Collate: 'MotifSetup-class.R' 'PlotSetPair-class.R'
        'PlotSetArray-class.R' 'PlotSetList-class.R'
        'add_local_files.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'
PackageStatus: Deprecated
git_url: https://git.bioconductor.org/packages/seqplots
git_branch: RELEASE_3_9
git_last_commit: 5702092
git_last_commit_date: 2019-06-12
Date/Publication: 2019-06-12
NeedsCompilation: no
Packaged: 2019-06-13 02:59:54 UTC; biocbuild
Author: Przemyslaw Stempor [aut, cph, cre]
Built: R 3.6.0; ; 2019-06-13 14:03:45 UTC; windows
