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

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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.

Author
Przemyslaw Stempor
Date of publication
None
Maintainer
Przemyslaw Stempor <ps562@cam.ac.uk>
License
GPL-3
Version
1.12.0
URLs

View on Bioconductor

Man pages

deployServerInstance
Prepares the instance of SeqPlots, that can be deployed to...
getPlotSetArray
Process genomic signal
ggHeatmapPlotWrapper
Wrapper function, plotting the heatmap
heatmapPlotWrapper
Wrapper function, plotting the heatmap
imPlot2
Modified image.plot function from "fields" package, the grey...
MotifSetup-class
MotifSetup Reference Class
num2bp
Converts numeric values to labels with base pairs units, i.e...
num2sci
Converts numeric values labels with metric system suffix, i.e...
plot
Generic plot function for SeqPlots package calsses
plotAverage
Create the average plot
plotHeatmap
Plot heatmap with optional clustering
plotMext
Wrapper function, plotting the average plot
PlotSetArray-class
PlotSetArray Reference Class
PlotSetList-class
PlotSetList Reference Class
PlotSetPair-class
PlotSetPair Reference Class
run
SeqPlots innitiation
seqplots
SeqPlots - An interactive tool for visualizing NGS signals...
seqplots-generic
SeqPlots generic methods

Files in this package

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
seqplots/inst/seqplots/www/css/images/back_disabled.png
seqplots/inst/seqplots/www/css/images/back_enabled.png
seqplots/inst/seqplots/www/css/images/back_enabled_hover.png
seqplots/inst/seqplots/www/css/images/forward_disabled.png
seqplots/inst/seqplots/www/css/images/forward_enabled.png
seqplots/inst/seqplots/www/css/images/forward_enabled_hover.png
seqplots/inst/seqplots/www/css/images/sort_asc.png
seqplots/inst/seqplots/www/css/images/sort_asc_disabled.png
seqplots/inst/seqplots/www/css/images/sort_both.png
seqplots/inst/seqplots/www/css/images/sort_desc.png
seqplots/inst/seqplots/www/css/images/sort_desc_disabled.png
seqplots/inst/seqplots/www/css/mask2.png
seqplots/inst/seqplots/www/css/style.css
seqplots/inst/seqplots/www/font
seqplots/inst/seqplots/www/font/FontAwesome.otf
seqplots/inst/seqplots/www/font/fontawesome-webfont.eot
seqplots/inst/seqplots/www/font/fontawesome-webfont.svg
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
seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_02.png
seqplots/inst/seqplots/www/help/img/01_QuickStart/01_QuickStart_03.png
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seqplots/inst/seqplots/www/help/img/03_01.png
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seqplots/inst/seqplots/www/help/img/06
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seqplots/inst/seqplots/www/help/img/08_01.png
seqplots/inst/seqplots/www/help/img/08_02.png
seqplots/inst/seqplots/www/help/img/08_03.png
seqplots/inst/seqplots/www/help/img/08_04.png
seqplots/inst/seqplots/www/help/img/08_05.png
seqplots/inst/seqplots/www/help/img/09_01.png
seqplots/inst/seqplots/www/help/img/09_02.png
seqplots/inst/seqplots/www/help/img/09_03.png
seqplots/inst/seqplots/www/help/img/09_04.png
seqplots/inst/seqplots/www/help/img/10_00.png
seqplots/inst/seqplots/www/help/img/10_01.png
seqplots/inst/seqplots/www/help/img/11_01.png
seqplots/inst/seqplots/www/help/img/SeqPlots_fig1_web.png
seqplots/inst/seqplots/www/help/img/fav.ico
seqplots/inst/seqplots/www/help/img/ico_full.png
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
seqplots/inst/seqplots/www/help/index_files/bootstrap-3.3.1/fonts/glyphicons-halflings-regular.svg
seqplots/inst/seqplots/www/help/index_files/bootstrap-3.3.1/fonts/glyphicons-halflings-regular.ttf
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