inst/seqplots/www/help/Home.md
In Przemol/seqplots: An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps
Interactive software for exploratory data analyses, pattern discovery and visualization in genomics.
Summary
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.
Key features
- Easy to use web interface (R or shell expertise not required)
- Web server or desktop versions
- Generates publication quality plots out of the box
- Plots average signals or heatmaps
- Accepts Wiggle, BedGraph, BigWiggle, and GFF and BED formats
- Calculates motif density from reference genome packages
- Tracks and features are searchable and old calculations stored
- Converts tracks to binary BigWiggle format for rapid data extraction and efficient storage
- Implemented using Shiny R framework providing internet browser reactive GUI and session based connectivity (websocets)
Issues and bugs
Please visit issue tracker to view currently know issues. To report a new issue/bug/feature request please click here. If the issue is connected to file upload please attach the file in the form.
Przemol/seqplots documentation built on May 14, 2022, 6:47 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Interactive software for exploratory data analyses, pattern discovery and visualization in genomics.
Summary
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.
Key features
- Easy to use web interface (R or shell expertise not required)
- Web server or desktop versions
- Generates publication quality plots out of the box
- Plots average signals or heatmaps
- Accepts Wiggle, BedGraph, BigWiggle, and GFF and BED formats
- Calculates motif density from reference genome packages
- Tracks and features are searchable and old calculations stored
- Converts tracks to binary BigWiggle format for rapid data extraction and efficient storage
- Implemented using Shiny R framework providing internet browser reactive GUI and session based connectivity (websocets)
Issues and bugs
Please visit issue tracker to view currently know issues. To report a new issue/bug/feature request please click here. If the issue is connected to file upload please attach the file in the form.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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