Package: scdataloader
scdataloaderAwesome single cell dataloader created by @jkobjectbuilt on top oflamindband the.mapped()function by Sergey:https://github.com/KoncopdThis data loader is designed to be used with:lamindband:scanpyanndataIt allows you to:load thousands of datasets containing millions of cells in a few seconds.preprocess the data per dataset and download it locally (normalization, filtering, etc.)create a more complex single cell datasetextend it to your needAboutthe idea is to use it to train models like scGPT / GeneFormer (and soon, scPrint ;)). It is:loading from lamindoing some dataset specific preprocessing if neededcreating a dataset object on top of .mapped() (that is needed for mapping genes, cell labels etc..)passing it to a dataloader object that can work with it correctlyCurrently one would have to use the preprocess function to make the dataset fit for different tools like scGPT / Geneformer. But I would want to enable it through different Collators. This is still missing and a WIP... (please do contribute!)Install it from PyPIpipinstallscdataloaderInstall it locally and run the notebooks:gitclonehttps://github.com/jkobject/scDataLoader.gitcdscDataLoader
poetryinstallthen run the notebooks with the poetry installed environmentUsagesee the notebooks indocs:load a datasetcreate a datasetDevelopmentRead theCONTRIBUTING.mdfile.GNU GENERAL PUBLIC LICENSE
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