Stempor P and Ahringer J. SeqPlots - Interactive software for exploratory data analyses, pattern discovery and visualization in genomics [version 1; referees: 2 approved, 1 approved with reservations]. Wellcome Open Res 2016, 1:14 doi: 10.12688/wellcomeopenres.10004.1
: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.
SeqPlots is a user-friendly exploratory data analysis (EDA) and visualization software for genomics. After choosing groups of signal and feature files and defining plotting parameters, users can generate profile plots of average signal or heat maps clustered using different algorithms in a matter of seconds through the graphical user interface (GUI) controls. SeqPlots accepts all major genomic file formats as input and can also generate and plot user defined motif densities. Profile plots and heatmaps are highly configurable and batch operations can be used to generate a large number of plots at once. SeqPlots is available as a GUI application for Mac or Windows and Linux, or as an R/Bioconductor package. It can also be deployed on a server for remote and collaborative usage. The analysis features and ease of use of SeqPlots encourages wide data exploration, which should aid the discovery of novel genomic associations.
Install develpment version from Bioconductor:
if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("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:
To start with R scripting mode:
The App bundle is an easy way to use SeqPlots for macOS, Win and Linux. It contains all R binaries and packages that SeqPlots depends on. Additionally, test tracks and genome annotations, and reference sequences for Drosophila melanogaster and Caenorhabditis elegans are included. Sequences for other organisms can be downloaded using a graphical user interface - follow the instructions here: http://przemol.github.io/seqplots/#genomes-managment
R project and Bioconductor
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