An interactive tool for visualizing track signals and sequence motif densities along genomic features using average plots and heatmaps
:exclamation: RELEASE NOTE :exclamation:
GitHub repository holds development version of SeqPlots. The release is available on Bioconductor. Please report the problem, bugs, unexpected behaviors and missing features using issue tracker.
The working demonstration preview of SeqPlots is available on ShinyApps.io: https://seqplots.shinyapps.io/seqplots/
Demo limits:
The SeqPlots is universal, web browser based tool for plotting average track signal (e.g. reads coverage) and sequence motif density over user specified genomic features. The data are visualized on linear plot, with error estimates as fields, or as series of heatmaps that can be sorted and clustered. The dual-purpose implementation allows running the software locally on desktop or deploying it on server. The unique features of our software are 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.
Install develpment version from Bioconductor:
source("http://bioconductor.org/biocLite.R")
biocLite("seqplots")
To install GitHub vesrion (in order to solve dependencies install from Bioconductor first):
if (!require("devtools")) install.packages("devtools")
devtools::install_github('przemol/seqplots', build_vignettes=FALSE)
To start web browser GUI:
library(seqplots)
run()
To start with R scripting mode:
?getPlotSetArry
Mac OS X bundle is an easy way to use SeqPlots for Mac OS X users. It contains R binaries pre-installed Bioconductor dependencies. Additionally, the reference genome for Caenorhabditis elegans is included. The sequences for other popular model organisms can be downloaded using graphical user interface.
Download the current version here: https://github.com/Przemol/seqplots_osx/releases/latest
The bundle requires OS X 10.6 (Snow Leopard) and above with X11 installed. X11 was included with OS X up to version 10.7 (Lion). OS X 10.8 (Mountain Lion) and above require installation of Xquartz package, see more here: http://support.apple.com/en-us/HT201341
R project and Bioconductor
JavaScript and CSS
Important conceptual contribution to the project
Server deployment
Publications containing figures made by SeqPlots
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