plotting the density of genetic elements along a chromosome using GTF files (ideally from Ensembl) as input and using REST API calls to Ensembl, OMA and STRING database (to be done).
It allows to use a GTF file as input and then to display mRNA, exon (in the second column). Maximum threshold per BIN from 200 non-overlapping bins respective to largest chromosomes defines highest intensity.
Visualizing all genes from an input GTF file and Ensembl Webservice calls to retrieve sequence for a gene as well as gene tree for a particular human gene.
Here we used the entire genes as input. Here, we show the amount of genes per bin that are tagged compared to the genes that are to be found within the given bin. If no candidate genes are provided, the overall distribution of genes is shown.
Or searching for candidate genes by uploading the candidate genes
The GTF can be taken from Ensembl and then any of the element types can be selected and visualized.
Ensembl provide a bunch of different endpoints to obtain data. We use some of these endpoints in Gexplora (https://rest.ensembl.org/).
The annotation was downloaded from Ensembl .
The annotation was downloaded from Ensembl .
and gene distribution was shown while also all other types can be shown in the density visualisation.
In Gexplora, we use tkinter for the graphical user interface, while we use numpy to be faster in calculating overlaps between elements of two arrays while requests is used to obtain data from endpoints of Ensembl.
- numpy
- requests
- tkinter
- json
For installation under Windows, you can use the "pip.exe" that can be normally found in the subdirectory "scripts" within the python installation. You can install Python packages using ``pip.exe install requests''-
To generate the executable to run: pip install https://github.com/pyinstaller/pyinstaller/archive/develop.zip