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TheJacksonLaboratory / isopretGO

Isoform function prediction and interpretation
https://thejacksonlaboratory.github.io/isopretGO/
GNU General Public License v3.0
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Input files provided for IsopretGUI out of date #151

Closed hansenp closed 8 months ago

hansenp commented 1 year ago

The documentation refers to a Zenodo repository (https://zenodo.org/record/6483996), which provides 100 input files for isopretGUI, which were created using HBA-Deals. These files are out of date. Due to changes in RNA-seq/HBA-Deals pipeline, the numbers of differentially expressed and spliced genes have changed. These files should be updated. Furthermore, the code for the pipeline used should be specified. Beyond HBA-Deals output files, isopretGUI requires additional input files that are provided in a second Zenodo repository (https://zenodo.org/record/6466530). These files should also be checked to make sure they are up to date and updated if necessary.

pnrobinson commented 10 months ago

@karleg Could we update the zenodo as described above? It would probably make sense to include the 100 input files and also the COVID files if possible. I think the files in the second repository are still up to date though?

karleg commented 10 months ago

I don't have an option to update, either because it's not possible or because the permissions are not set that way. If it's not possible to update, I could create another archive?

hansenp commented 10 months ago

In the Zenodo documentation it says:

We do not allow modification (add, remove, modify) of files after it has been published. Instead, you can use our versioning to create a new version of the record.

pnrobinson commented 8 months ago

The zenodo has been updated in the manuscript.