search

theislab / spapros

Python package for Probe set selection for targeted spatial transcriptomics.
MIT License
23 stars 6 forks source link

adapter tutorials to new framework #357

Open lisa-sousa opened 4 months ago

lisa-sousa commented 4 months ago

PR Checklist

Description of changes

Changed and adapted the end to end selection tutorials to the oligo designer tool suite API. Updated dependency description and added examples for config files.

Technical details

New API is significantly faster and requires significantly less memory. The memory consumption is now limited by a maximum number of entries that is loaded into ram. The db_max_memory defines how many entries are loaded and has to be at least _2*njob+1 to run without errors. db_max_memory is set internally in the pipeline to the value describes above. If the memory consumption is too high because too many entries are loaded into ram the performance of the program will be significantly decreased and hence its adviced to decrease the number of jobs n_jobs. For a laptop with 8cores and 16GB RAM and values of n_jobs=4 is a good value.

review-notebook-app[bot] commented 4 months ago

Check out this pull request on  ReviewNB

See visual diffs & provide feedback on Jupyter Notebooks.

Powered by ReviewNB

github-actions[bot] commented 4 months ago

Hi @lisa-sousa,

It looks like this pull-request is has been made against the theislab/spapros master or main branch. The master/main branch should always contain code from the latest release. Because of this, PRs to master/main are only allowed if they come from any theislab/spapros release or patch branch.

You do not need to close this PR, you can change the target branch to development by clicking the "Edit" button at the top of this page.

Thanks again for your contribution!