Change tutorial data download links from nextcloud to Hugging Face datasets - #203
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example at Hugging Face dataset Replaces the manual 8GB zip download with hf_hub_download calls against autoencodix/tcga for the bulk-sequencing example and adds huggingface_hub as an explicit dependency Ref #171
Bring in beta-scaling fix (3c01369) for var_loss visualization
Replaces the expired scadsai-nextcloud download links for GSE84133 (Maskix), the TCGA multi-omics + ontology files (Ontix) and the TCGA + xmodalix image bundle (XModalix) with hf_hub_download calls against autoencodix/pancreas-fang and autoencodix/tcga.
…ta-for-inputdatatutorial
…utorials at Huggingface
alicia01101
marked this pull request as draft
August 5, 2026 09:38
jan-forest
marked this pull request as ready for review
August 6, 2026 07:59
… into 171-change-example-data-for-inputdatatutorial
…beta_tc settings to Disentanglix Tutorial
alicia01101
marked this pull request as draft
August 18, 2026 13:36
alicia01101
marked this pull request as ready for review
August 18, 2026 13:39
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This PR contains changes to replace expired scads nextcloud tutorial data download links with Hugging Face dataset downloads
Changes in this PR:
Ontix.ipynb,XModalix.ipynb→autoencodix/tcga(+ontology/,xmodalix/subfolders)Maskix.ipynb→autoencodix/pancreas-fangUsingPreTrainedModels.ipynb→autoencodix/census-lungInputDataTutorials.ipynb(bulk section) →autoencodix/tcgaConfigTutorial.ipynb,ExplainStep.ipynb→autoencodix/tcgaPipelineOutputTutorial.ipynb,MemoryEfficientSaving.ipynb,InputDataTutorials.ipynb(image section) →autoencodix/tcga+xmodalix/(RNA + clinical joined with image mapping + extracted image zip)Varix.ipynb→ switching from mockEXAMPLE_MULTI_SCtoautoencodix/census-lungDisentanglix.ipynb→ same switchVanillix.ipynb→autoencodix/tcgaStackix.ipynb→autoencodix/tcga(RNA + DNA methylation + clinical data)Imagix.ipynb→autoencodix/mnistIn progress:
InputDataTutorials.ipynbsingle-cell section (Sc-2-mini.h5ad)Addresses #171, #129