Question: GUI framework for sequence data analysis and visulaization
2
gravatar for Pappu
2.7 years ago by
Pappu1.8k
Pappu1.8k wrote:

I am wondering if there is any open source sequence data visualization and data analysis GUI framework preferably in python in which can be easily extended to add custom tools. I am looking for open source alternatives to Geneious or CLC.

The problem is that there are too many bioinformatics tools available. I need a GUI interface where I can easily add custom tools. Thanks.

python • 1.2k views
ADD COMMENTlink modified 2.7 years ago by vranckx.katleen40 • written 2.7 years ago by Pappu1.8k

Check DNAplotlib.

ADD REPLYlink written 2.7 years ago by h.mon19k
0
gravatar for Pierre Lindenbaum
2.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum112k wrote:

https://usegalaxy.org/

ADD COMMENTlink written 2.7 years ago by Pierre Lindenbaum112k

Galaxy does not seem to have nice interactive data visualization and editing.

ADD REPLYlink written 2.7 years ago by Pappu1.8k
1

Galaxy has:


and much more.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by martenson380

Sounds cool! Yet not sure about the possibility of interactive editing of data,  sequence alignment etc.

ADD REPLYlink written 2.7 years ago by Pappu1.8k
1

iPython and Jupyter are designed for interactive editing

other tools generally work with Galaxy Datasets that you can modify with any other Galaxy tools (including basic text-manipulation ones) See https://usegalaxy.org .

 

ADD REPLYlink written 2.7 years ago by martenson380
0
gravatar for vranckx.katleen
2.7 years ago by
Belgium
vranckx.katleen40 wrote:

I think you will get more specific answers if you give more details on what type of visualisations you expect and what kind of data you are working on, as typically, a specific tool is specialised in a specific type of analysis/data. Are you working with sanger sequences, Illumina, PacBio,...; whole genome, prokaryotic, eaukaryotic, metagenome,... 

We develop a software called BioNumerics, that is neither open nor free, but it does offer nice visualisations of all types of data (focus is on prokaryotes) and there is a Python editor that allows you to add your own functionality. But this is also the case for CLC and Geneious, so I'm not sure what it is exactly that you are lacking in these softwares?

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by vranckx.katleen40

Just looking for an open source one to add plugins of softwares I use.
 

ADD REPLYlink written 2.7 years ago by Pappu1.8k
1

Galaxy visualization plugins: https://wiki.galaxyproject.org/Develop/Visualizations

Biojs to Galaxy: https://github.com/biojs/biojs2galaxy http://biojs.net/

ADD REPLYlink written 2.7 years ago by martenson380
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