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biocypher / sc2cl

Knowledge graph for mapping and harmonising single cell experiments
MIT License
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Develop Pipeline from raw scSeq data to Annotation #12

Closed tim-schubert closed 1 year ago

tim-schubert commented 1 year ago

Seurat works well for handling data. The output is a .csv file per cell with the gene expression listed from highest to lowest count. This part could be augmented by integrating other packages for handling single cell data in the future.

slobentanzer commented 1 year ago

Hi @tim-schubert, where is the code for this?

tim-schubert commented 1 year ago

Hi @slobentanzer, @JonasJuergensen will push it alongside the rest of the code.

slobentanzer commented 1 year ago

Alright. Bear in mind that I will still need to go over it to grade it, and Sandy wants the form returned tomorrow. The official deadline for the code was yesterday.

tim-schubert commented 1 year ago

Thanks, I will remind him.