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Thursday, November 3, 2022

5 tools to visualize genomic datasets

 1. Karyoploter https://bernatgel.github.io/karyoploter_tutorial/Tutorial/PlotCoverage/PlotCoverage.html I used that to plot single-cell ATACseq tracks https://github.com/crazyhottommy/scATACutils/#plot-atacseq-tracks-for-each-cluster-of-cells, more examples https://rpubs.com/crazyhottommy/scATAC_tracks

2. plotgardener is a genomic data visualization package for R. Using `grid` graphics, `plotgardener` empowers users to programmatically and flexibly generate multi-panel figures 

https://github.com/PhanstielLab/plotgardener 

3. The goal of **g(r)osling** https://github.com/gosling-lang/grosling is to help you build interactive genomics visualizations with [Gosling](https://github.com/gosling-lang/gosling.js). This package uses [reticulate](https://rstudio.github.io/reticulate/) to provide an interface to the [Gos](https://github.com/gosling-lang/gos) Python package. https://github.com/gosling-lang/grosling

4.  Intervene: a tool for intersection and visualization of multiple gene or genomic region sets 

 https://bitbucket.org/CBGR/intervene/src/master/

 5. https://42basepairs.com/ saw it yesterday by @RobAboukhalil

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