seqplots: An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps
Version 1.13.0

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
Bioconductor views ChIPSeq RNASeq Sequencing Software Visualization
Date of publicationNone
MaintainerPrzemyslaw Stempor <ps562@cam.ac.uk>
LicenseGPL-3
Version1.13.0
URL http://github.com/przemol/seqplots
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("seqplots")

Getting started

README.md
SeqPlots R workflow
SeqPlots R workflow

Popular man pages

imPlot2: Modified image.plot function from "fields" package, the grey...
plot: Generic plot function for SeqPlots package calsses
plotAverage: Create the average plot
PlotSetArray-class: PlotSetArray Reference Class
PlotSetList-class: PlotSetList Reference Class
run: SeqPlots innitiation
seqplots: SeqPlots - An interactive tool for visualizing NGS signals...
See all...

All man pages Function index File listing

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

Functions

MotifSetup Man page
MotifSetup-class Man page
PlotSetArray Man page
PlotSetArray-class Man page
PlotSetList Man page
PlotSetList-class Man page
PlotSetPair Man page
PlotSetPair-class Man page
[,PlotSetArray,ANY,missing,ANY-method Man page
[,PlotSetArray,ANY,vector,ANY-method Man page
[,PlotSetList,ANY,ANY,ANY-method Man page
[[,PlotSetArray,ANY,ANY-method Man page
[[,PlotSetList,ANY,ANY-method Man page
deployServerInstance Man page Source code
getPlotSetArray Man page Source code
getSF Source code
ggHeatmapPlotWrapper Man page Source code
heatmapPlotWrapper Man page Source code
imPlot2 Man page Source code
num2bp Man page Source code
num2sci Man page Source code
onAttach Source code
plot Man page
plot,PlotSetArray,ANY-method Man page
plot,PlotSetList,ANY-method Man page
plot,PlotSetPair,ANY-method Man page
plotAverage Man page
plotAverage,PlotSetArray-method Man page
plotAverage,PlotSetList-method Man page
plotAverage,PlotSetPair-method Man page
plotAverage,list-method Man page
plotHeatmap Man page
plotHeatmap,PlotSetArray-method Man page
plotHeatmap,PlotSetList-method Man page
plotHeatmap,PlotSetPair-method Man page
plotHeatmap,list-method Man page
plotMext Man page Source code
run Man page Source code
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
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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
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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
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inst/seqplots/www/help/img/01_QuickStart
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inst/seqplots/www/help/index_files
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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
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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
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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
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inst/seqplots/www/js/modal_events.js
inst/seqplots/www/js/tmpl.min.js
inst/seqplots/www/js/tutorial.js
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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
seqplots documentation built on May 20, 2017, 9:38 p.m.

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