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

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("seqplots")
AuthorPrzemyslaw Stempor
Bioconductor views ChIPSeq RNASeq Sequencing Software Visualization
Date of publicationNone
MaintainerPrzemyslaw Stempor <ps562@cam.ac.uk>
LicenseGPL-3
Version1.12.0
http://github.com/przemol/seqplots

View on Bioconductor

Functions

deployServerInstance Man page
getPlotSetArray Man page
ggHeatmapPlotWrapper Man page
heatmapPlotWrapper Man page
imPlot2 Man page
MotifSetup Man page
MotifSetup-class Man page
num2bp Man page
num2sci Man page
plot Man page
plotAverage Man page
plotAverage,list-method Man page
plotAverage,PlotSetArray-method Man page
plotAverage,PlotSetList-method Man page
plotAverage,PlotSetPair-method Man page
plotHeatmap Man page
plotHeatmap,list-method Man page
plotHeatmap,PlotSetArray-method Man page
plotHeatmap,PlotSetList-method Man page
plotHeatmap,PlotSetPair-method Man page
plotMext Man page
plot,PlotSetArray,ANY-method Man page
plot,PlotSetList,ANY-method Man page
plot,PlotSetPair,ANY-method Man page
PlotSetArray Man page
[[,PlotSetArray,ANY,ANY-method Man page
[,PlotSetArray,ANY,missing,ANY-method Man page
[,PlotSetArray,ANY,vector,ANY-method Man page
PlotSetArray-class Man page
PlotSetList Man page
[,PlotSetList,ANY,ANY,ANY-method Man page
[[,PlotSetList,ANY,ANY-method Man page
PlotSetList-class Man page
PlotSetPair Man page
PlotSetPair-class Man page
run Man page
seqplots Man page
seqplots-generic Man page
seqplots-package Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/MotifSetup-class.R R/PlotSetArray-class.R R/PlotSetList-class.R R/PlotSetPair-class.R R/deployServerInstance.R R/generic_methods.R R/getPlotSetArray.R R/helper_functions.R R/int_getSF.R R/int_ggHeatmapPlotWrapper.R R/int_heatmapPlotWrapper.R R/int_imPlot2.R R/int_plotMext.R R/plotAverage.R R/plotHeatmap.R R/run.R R/seqplots-package.R R/zzz.R
README.md
build
build/vignette.rds
inst
inst/doc
inst/doc/QuickStart.R
inst/doc/QuickStart.Rmd
inst/doc/QuickStart.html
inst/doc/SeqPlotsGUI.R
inst/doc/SeqPlotsGUI.Rmd
inst/doc/SeqPlotsGUI.html
inst/extdata
inst/extdata/GSM1208360_chrI_100Kb_q5_sample.bw
inst/extdata/GSM1208361_chrI_100Kb_PeakCalls.bed
inst/extdata/Transcripts_ce10_chrI_100Kb.bed
inst/extdata/precalc_plotset.Rdata
inst/seqplots
inst/seqplots/functions
inst/seqplots/functions/LOCAL
inst/seqplots/functions/LOCAL/mceval.R inst/seqplots/functions/LOCAL/server_plotHeatmap.R inst/seqplots/functions/LOCAL/server_plotLineplot.R inst/seqplots/functions/doFileOperations.R inst/seqplots/functions/mcCalcStart_calculations.R inst/seqplots/functions/mcDoParallel_plotting.R inst/seqplots/functions/renderHTMLgrid.R inst/seqplots/global.R inst/seqplots/server.R inst/seqplots/server_config.R
inst/seqplots/ui
inst/seqplots/ui.R
inst/seqplots/ui/DataTablesColumnSetup.js
inst/seqplots/ui/DataTablesToolsSetup.js
inst/seqplots/ui/FileManagementModal.R
inst/seqplots/ui/loadModal.html
inst/seqplots/www
inst/seqplots/www/biodalliance.html
inst/seqplots/www/color
inst/seqplots/www/color/arrow.gif
inst/seqplots/www/color/cross.gif
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inst/seqplots/www/color/jscolor.js
inst/seqplots/www/css
inst/seqplots/www/css/DT_bootstrap.css
inst/seqplots/www/css/NewFont.woff
inst/seqplots/www/css/TableTools.css
inst/seqplots/www/css/font-awesome.min.css
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inst/seqplots/www/css/style.css
inst/seqplots/www/font
inst/seqplots/www/font/FontAwesome.otf
inst/seqplots/www/font/fontawesome-webfont.eot
inst/seqplots/www/font/fontawesome-webfont.svg
inst/seqplots/www/font/fontawesome-webfont.ttf
inst/seqplots/www/font/fontawesome-webfont.woff
inst/seqplots/www/help
inst/seqplots/www/help/AdvOup.md
inst/seqplots/www/help/Batch.md
inst/seqplots/www/help/Errors.md
inst/seqplots/www/help/Files.md
inst/seqplots/www/help/GUIplottingControls.md
inst/seqplots/www/help/Genomes.md
inst/seqplots/www/help/Heatmaps.md
inst/seqplots/www/help/Home.md
inst/seqplots/www/help/Home2.md
inst/seqplots/www/help/Install_Docker.md
inst/seqplots/www/help/Install_OSX.md
inst/seqplots/www/help/Install_R.md
inst/seqplots/www/help/Install_server.md
inst/seqplots/www/help/Outputs.md
inst/seqplots/www/help/PlotSets.md
inst/seqplots/www/help/Plotting.md
inst/seqplots/www/help/QuickStart.md
inst/seqplots/www/help/References.md
inst/seqplots/www/help/SaveAndLoad.md
inst/seqplots/www/help/Terms.md
inst/seqplots/www/help/Versions.md
inst/seqplots/www/help/help.html
inst/seqplots/www/help/img
inst/seqplots/www/help/img/01_QuickStart
inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_01.png
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inst/seqplots/www/help/img/fav.ico
inst/seqplots/www/help/img/ico_full.png
inst/seqplots/www/help/img/ico_full_color.png
inst/seqplots/www/help/img/palettes.png
inst/seqplots/www/help/index_files
inst/seqplots/www/help/index_files/bootstrap-3.3.1
inst/seqplots/www/help/index_files/bootstrap-3.3.1/css
inst/seqplots/www/help/index_files/bootstrap-3.3.1/css/bootstrap.min.css
inst/seqplots/www/help/index_files/bootstrap-3.3.1/css/fonts
inst/seqplots/www/help/index_files/bootstrap-3.3.1/css/fonts/Ubuntu.ttf
inst/seqplots/www/help/index_files/bootstrap-3.3.1/css/united.min.css
inst/seqplots/www/help/index_files/bootstrap-3.3.1/fonts
inst/seqplots/www/help/index_files/bootstrap-3.3.1/fonts/glyphicons-halflings-regular.eot
inst/seqplots/www/help/index_files/bootstrap-3.3.1/fonts/glyphicons-halflings-regular.svg
inst/seqplots/www/help/index_files/bootstrap-3.3.1/fonts/glyphicons-halflings-regular.ttf
inst/seqplots/www/help/index_files/bootstrap-3.3.1/fonts/glyphicons-halflings-regular.woff
inst/seqplots/www/help/index_files/bootstrap-3.3.1/js
inst/seqplots/www/help/index_files/bootstrap-3.3.1/js/bootstrap.min.js
inst/seqplots/www/help/index_files/bootstrap-3.3.1/shim
inst/seqplots/www/help/index_files/bootstrap-3.3.1/shim/html5shiv.min.js
inst/seqplots/www/help/index_files/bootstrap-3.3.1/shim/respond.min.js
inst/seqplots/www/help/index_files/jquery-1.11.0
inst/seqplots/www/help/index_files/jquery-1.11.0/jquery.min.js
inst/seqplots/www/help/style.css
inst/seqplots/www/help/themes
inst/seqplots/www/js
inst/seqplots/www/js/DataTables
inst/seqplots/www/js/DataTables/DT_bootstrap.js
inst/seqplots/www/js/DataTables/DT_filter.js
inst/seqplots/www/js/DataTables/dataTables.tableTools.min.js
inst/seqplots/www/js/DataTables/jquery.dataTables.js
inst/seqplots/www/js/actionbutton.js
inst/seqplots/www/js/afterHTMLgridrender.js
inst/seqplots/www/js/color.js
inst/seqplots/www/js/jquery.ba-throttle-debounce.js
inst/seqplots/www/js/jquery.cookie.js
inst/seqplots/www/js/jquery.lettering.js
inst/seqplots/www/js/js_addons.js
inst/seqplots/www/js/load_finished.js
inst/seqplots/www/js/modal_events.js
inst/seqplots/www/js/tmpl.min.js
inst/seqplots/www/js/tutorial.js
inst/seqplots/www/outro.html
inst/seqplots/www/tutorial.html
inst/seqplots/www/upload
inst/seqplots/www/upload/css
inst/seqplots/www/upload/css/jquery.fileupload-ui-noscript.css
inst/seqplots/www/upload/css/jquery.fileupload-ui.css
inst/seqplots/www/upload/css/style.css
inst/seqplots/www/upload/img
inst/seqplots/www/upload/img/loading.gif
inst/seqplots/www/upload/img/progressbar.gif
inst/seqplots/www/upload/js
inst/seqplots/www/upload/js/cors
inst/seqplots/www/upload/js/cors/jquery.postmessage-transport.js
inst/seqplots/www/upload/js/cors/jquery.xdr-transport.js
inst/seqplots/www/upload/js/jquery.fileupload-fp.js
inst/seqplots/www/upload/js/jquery.fileupload-ui.js
inst/seqplots/www/upload/js/jquery.fileupload-validate.js
inst/seqplots/www/upload/js/jquery.fileupload.js
inst/seqplots/www/upload/js/jquery.iframe-transport.js
inst/seqplots/www/upload/js/main.js
inst/seqplots/www/upload/js/md5.js
inst/seqplots/www/upload/js/vendor
inst/seqplots/www/upload/js/vendor/jquery.ui.widget.js
inst/seqplots/www/upload/upload.html
man
man/MotifSetup-class.Rd man/PlotSetArray-class.Rd man/PlotSetList-class.Rd man/PlotSetPair-class.Rd man/deployServerInstance.Rd man/getPlotSetArray.Rd man/ggHeatmapPlotWrapper.Rd man/heatmapPlotWrapper.Rd man/imPlot2.Rd man/num2bp.Rd man/num2sci.Rd man/plot.Rd man/plotAverage.Rd man/plotHeatmap.Rd man/plotMext.Rd man/run.Rd man/seqplots-generic.Rd man/seqplots.Rd
tests
tests/test-all.R
tests/testthat
tests/testthat/test1.R tests/testthat/testGUI.R
vignettes
vignettes/QuickStart.Rmd
vignettes/SeqPlotsGUI.Rmd

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