Sample number and text extension update #125
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| @@ -94,7 +94,7 @@ The ADT by cell counts matrix is normalized by first determining the ambient pro | |||
| We skip normalization for cells with low-quality ADT expression, as indicated by `DropletUtils::cleanTagCounts()`. | |||
| Although `scpca-nf` normalizes ADT counts, the workflow does not perform any dimensionality reduction of ADT data; only the RNA counts data are used as input for dimensionality reduction. | |||
| The normalized ADT data are saved as an `altExp` within the processed `SingleCellExperiment` containing the normalized RNA data and is output to a file with the suffix `_processed.rds`. | |||
| All files containing `SingleCellExperiment` objects and associated `altExp` objects are converted to `AnnData` objects and exported as separate RNA (`_rna.hdf5`) and ADT (`_adt.hdf5`) `AnnData` objects. | |||
| All files containing `SingleCellExperiment` objects and associated `altExp` objects are converted to `AnnData` objects and exported as separate RNA (`_rna.h5ad`) and ADT (`_adt.h5ad`) `AnnData` objects. | |||
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Can you file issues tracking the change to the figures in https://github.com/AlexsLemonade/scpca-paper-figures/ as well please? The little icons say HDF5.
jaclyn-taroni
approved these changes
Dec 16, 2024
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Click the link below to download the manuscript build as a ZIP file. There were 1 spelling errors. |
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…update [ci skip] This build is based on b74a970. This commit was created by the following CI build and job: https://github.com/AlexsLemonade/ScPCA-manuscript/commit/b74a9709211a03be1151739c21a7b4854848f34c/checks https://github.com/AlexsLemonade/ScPCA-manuscript/actions/runs/12377707472
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…update [ci skip] This build is based on b74a970. This commit was created by the following CI build and job: https://github.com/AlexsLemonade/ScPCA-manuscript/commit/b74a9709211a03be1151739c21a7b4854848f34c/checks https://github.com/AlexsLemonade/ScPCA-manuscript/actions/runs/12377707472
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Closes #123 and closes #122
Here I just updated the statements that summarized the total samples and diseases found on the Portal to be
700 samples from 55 types of cancer. We probably could leave it to beover 50 types of cancerif we prefer that?While I was here I updated the extensions for the
.h5adfiles in all the places I could find.The only other number updates should be the diagnosis and modality breakdown in the first section of the results. I plan to do that after I update the figure as a separate PR to address #124.