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.

AuthorPrzemyslaw Stempor
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

seqplots/DESCRIPTION
seqplots/NAMESPACE
seqplots/NEWS
seqplots/R
seqplots/R/MotifSetup-class.R seqplots/R/PlotSetArray-class.R seqplots/R/PlotSetList-class.R seqplots/R/PlotSetPair-class.R seqplots/R/deployServerInstance.R seqplots/R/generic_methods.R seqplots/R/getPlotSetArray.R seqplots/R/helper_functions.R seqplots/R/int_getSF.R seqplots/R/int_ggHeatmapPlotWrapper.R seqplots/R/int_heatmapPlotWrapper.R seqplots/R/int_imPlot2.R seqplots/R/int_plotMext.R seqplots/R/plotAverage.R seqplots/R/plotHeatmap.R seqplots/R/run.R seqplots/R/seqplots-package.R seqplots/R/zzz.R
seqplots/README.md
seqplots/build
seqplots/build/vignette.rds
seqplots/inst
seqplots/inst/doc
seqplots/inst/doc/QuickStart.R
seqplots/inst/doc/QuickStart.Rmd
seqplots/inst/doc/QuickStart.html
seqplots/inst/doc/SeqPlotsGUI.R
seqplots/inst/doc/SeqPlotsGUI.Rmd
seqplots/inst/doc/SeqPlotsGUI.html
seqplots/inst/extdata
seqplots/inst/extdata/GSM1208360_chrI_100Kb_q5_sample.bw
seqplots/inst/extdata/GSM1208361_chrI_100Kb_PeakCalls.bed
seqplots/inst/extdata/Transcripts_ce10_chrI_100Kb.bed
seqplots/inst/extdata/precalc_plotset.Rdata
seqplots/inst/seqplots
seqplots/inst/seqplots/functions
seqplots/inst/seqplots/functions/LOCAL
seqplots/inst/seqplots/functions/LOCAL/mceval.R
seqplots/inst/seqplots/functions/LOCAL/server_plotHeatmap.R
seqplots/inst/seqplots/functions/LOCAL/server_plotLineplot.R
seqplots/inst/seqplots/functions/doFileOperations.R
seqplots/inst/seqplots/functions/mcCalcStart_calculations.R
seqplots/inst/seqplots/functions/mcDoParallel_plotting.R
seqplots/inst/seqplots/functions/renderHTMLgrid.R
seqplots/inst/seqplots/global.R
seqplots/inst/seqplots/server.R
seqplots/inst/seqplots/server_config.R
seqplots/inst/seqplots/ui
seqplots/inst/seqplots/ui.R
seqplots/inst/seqplots/ui/DataTablesColumnSetup.js
seqplots/inst/seqplots/ui/DataTablesToolsSetup.js
seqplots/inst/seqplots/ui/FileManagementModal.R
seqplots/inst/seqplots/ui/loadModal.html
seqplots/inst/seqplots/www
seqplots/inst/seqplots/www/biodalliance.html
seqplots/inst/seqplots/www/color
seqplots/inst/seqplots/www/color/arrow.gif
seqplots/inst/seqplots/www/color/cross.gif
seqplots/inst/seqplots/www/color/hs.png
seqplots/inst/seqplots/www/color/hv.png
seqplots/inst/seqplots/www/color/jscolor.js
seqplots/inst/seqplots/www/css
seqplots/inst/seqplots/www/css/DT_bootstrap.css
seqplots/inst/seqplots/www/css/NewFont.woff
seqplots/inst/seqplots/www/css/TableTools.css
seqplots/inst/seqplots/www/css/font-awesome.min.css
seqplots/inst/seqplots/www/css/images
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seqplots/inst/seqplots/www/css/style.css
seqplots/inst/seqplots/www/font
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seqplots/inst/seqplots/www/font/fontawesome-webfont.ttf
seqplots/inst/seqplots/www/font/fontawesome-webfont.woff
seqplots/inst/seqplots/www/help
seqplots/inst/seqplots/www/help/AdvOup.md
seqplots/inst/seqplots/www/help/Batch.md
seqplots/inst/seqplots/www/help/Errors.md
seqplots/inst/seqplots/www/help/Files.md
seqplots/inst/seqplots/www/help/GUIplottingControls.md
seqplots/inst/seqplots/www/help/Genomes.md
seqplots/inst/seqplots/www/help/Heatmaps.md
seqplots/inst/seqplots/www/help/Home.md
seqplots/inst/seqplots/www/help/Home2.md
seqplots/inst/seqplots/www/help/Install_Docker.md
seqplots/inst/seqplots/www/help/Install_OSX.md
seqplots/inst/seqplots/www/help/Install_R.md
seqplots/inst/seqplots/www/help/Install_server.md
seqplots/inst/seqplots/www/help/Outputs.md
seqplots/inst/seqplots/www/help/PlotSets.md
seqplots/inst/seqplots/www/help/Plotting.md
seqplots/inst/seqplots/www/help/QuickStart.md
seqplots/inst/seqplots/www/help/References.md
seqplots/inst/seqplots/www/help/SaveAndLoad.md
seqplots/inst/seqplots/www/help/Terms.md
seqplots/inst/seqplots/www/help/Versions.md
seqplots/inst/seqplots/www/help/help.html
seqplots/inst/seqplots/www/help/img
seqplots/inst/seqplots/www/help/img/01_QuickStart
seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_01.png
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seqplots/inst/seqplots/www/help/img/SeqPlots_fig1_web.png
seqplots/inst/seqplots/www/help/img/fav.ico
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seqplots/inst/seqplots/www/help/img/ico_full_color.png
seqplots/inst/seqplots/www/help/img/palettes.png
seqplots/inst/seqplots/www/help/index_files
seqplots/inst/seqplots/www/help/index_files/bootstrap-3.3.1
seqplots/inst/seqplots/www/help/index_files/bootstrap-3.3.1/css
seqplots/inst/seqplots/www/help/index_files/bootstrap-3.3.1/css/bootstrap.min.css
seqplots/inst/seqplots/www/help/index_files/bootstrap-3.3.1/css/fonts
seqplots/inst/seqplots/www/help/index_files/bootstrap-3.3.1/css/fonts/Ubuntu.ttf
seqplots/inst/seqplots/www/help/index_files/bootstrap-3.3.1/css/united.min.css
seqplots/inst/seqplots/www/help/index_files/bootstrap-3.3.1/fonts
seqplots/inst/seqplots/www/help/index_files/bootstrap-3.3.1/fonts/glyphicons-halflings-regular.eot
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seqplots/inst/seqplots/www/help/index_files/bootstrap-3.3.1/fonts/glyphicons-halflings-regular.woff
seqplots/inst/seqplots/www/help/index_files/bootstrap-3.3.1/js
seqplots/inst/seqplots/www/help/index_files/bootstrap-3.3.1/js/bootstrap.min.js
seqplots/inst/seqplots/www/help/index_files/bootstrap-3.3.1/shim
seqplots/inst/seqplots/www/help/index_files/bootstrap-3.3.1/shim/html5shiv.min.js
seqplots/inst/seqplots/www/help/index_files/bootstrap-3.3.1/shim/respond.min.js
seqplots/inst/seqplots/www/help/index_files/jquery-1.11.0
seqplots/inst/seqplots/www/help/index_files/jquery-1.11.0/jquery.min.js
seqplots/inst/seqplots/www/help/style.css
seqplots/inst/seqplots/www/help/themes
seqplots/inst/seqplots/www/js
seqplots/inst/seqplots/www/js/DataTables
seqplots/inst/seqplots/www/js/DataTables/DT_bootstrap.js
seqplots/inst/seqplots/www/js/DataTables/DT_filter.js
seqplots/inst/seqplots/www/js/DataTables/dataTables.tableTools.min.js
seqplots/inst/seqplots/www/js/DataTables/jquery.dataTables.js
seqplots/inst/seqplots/www/js/actionbutton.js
seqplots/inst/seqplots/www/js/afterHTMLgridrender.js
seqplots/inst/seqplots/www/js/color.js
seqplots/inst/seqplots/www/js/jquery.ba-throttle-debounce.js
seqplots/inst/seqplots/www/js/jquery.cookie.js
seqplots/inst/seqplots/www/js/jquery.lettering.js
seqplots/inst/seqplots/www/js/js_addons.js
seqplots/inst/seqplots/www/js/load_finished.js
seqplots/inst/seqplots/www/js/modal_events.js
seqplots/inst/seqplots/www/js/tmpl.min.js
seqplots/inst/seqplots/www/js/tutorial.js
seqplots/inst/seqplots/www/outro.html
seqplots/inst/seqplots/www/tutorial.html
seqplots/inst/seqplots/www/upload
seqplots/inst/seqplots/www/upload/css
seqplots/inst/seqplots/www/upload/css/jquery.fileupload-ui-noscript.css
seqplots/inst/seqplots/www/upload/css/jquery.fileupload-ui.css
seqplots/inst/seqplots/www/upload/css/style.css
seqplots/inst/seqplots/www/upload/img
seqplots/inst/seqplots/www/upload/img/loading.gif
seqplots/inst/seqplots/www/upload/img/progressbar.gif
seqplots/inst/seqplots/www/upload/js
seqplots/inst/seqplots/www/upload/js/cors
seqplots/inst/seqplots/www/upload/js/cors/jquery.postmessage-transport.js
seqplots/inst/seqplots/www/upload/js/cors/jquery.xdr-transport.js
seqplots/inst/seqplots/www/upload/js/jquery.fileupload-fp.js
seqplots/inst/seqplots/www/upload/js/jquery.fileupload-ui.js
seqplots/inst/seqplots/www/upload/js/jquery.fileupload-validate.js
seqplots/inst/seqplots/www/upload/js/jquery.fileupload.js
seqplots/inst/seqplots/www/upload/js/jquery.iframe-transport.js
seqplots/inst/seqplots/www/upload/js/main.js
seqplots/inst/seqplots/www/upload/js/md5.js
seqplots/inst/seqplots/www/upload/js/vendor
seqplots/inst/seqplots/www/upload/js/vendor/jquery.ui.widget.js
seqplots/inst/seqplots/www/upload/upload.html
seqplots/man
seqplots/man/MotifSetup-class.Rd seqplots/man/PlotSetArray-class.Rd seqplots/man/PlotSetList-class.Rd seqplots/man/PlotSetPair-class.Rd seqplots/man/deployServerInstance.Rd seqplots/man/getPlotSetArray.Rd seqplots/man/ggHeatmapPlotWrapper.Rd seqplots/man/heatmapPlotWrapper.Rd seqplots/man/imPlot2.Rd seqplots/man/num2bp.Rd seqplots/man/num2sci.Rd seqplots/man/plot.Rd seqplots/man/plotAverage.Rd seqplots/man/plotHeatmap.Rd seqplots/man/plotMext.Rd seqplots/man/run.Rd seqplots/man/seqplots-generic.Rd seqplots/man/seqplots.Rd
seqplots/tests
seqplots/tests/test-all.R
seqplots/tests/testthat
seqplots/tests/testthat/test1.R
seqplots/tests/testthat/testGUI.R
seqplots/vignettes
seqplots/vignettes/QuickStart.Rmd
seqplots/vignettes/SeqPlotsGUI.Rmd

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