Commit History

  1. Upload annotation_human_G029.gtf with huggingface_hub

    7dc70e4

  1. Commit before changing file permissions.

    5d61a87

  1. Moved metric-tabular code and notebooks into main branch of metric-tabular repo. Consolidated notebooks for datasets in notebooks/ leaving only dataset files in top level dir.

    35dfebc

  1. Added padding to PerceiverTabularTokenizer.

    6e90a4a
  2. Added padding to PerceiverTabularTokenizer.

    ad8fa4c
  3. Added padding to PerceiverTabularTokenizer.

    1f60c5d
  4. Tokenizer and TPM finished. Still designing dataset object.

    1496d6b

  1. Added logic for converting to llvm using scipy. This can surely be done faster outside of python, but don't overoptimize. Strangely, the libsvm, svmlite file for BRCA is larger than the dense csv. This may be because we're storing large integers. May be less after normalization. It may simplly be that the count data is not as sparse as imagined. We really need to reduce to the subset of genes available for gene2vec intersection HiG2Vec, and that will greatly reduce the size of both. The libsvm format is good for text processing, I think but csr matrices or even dense matrices could be just as good if the sparsity is not so bad.

    81aebce
  2. Re-added sra_index.json.

    31f0c22
  3. Renamed sra_index.json.

    0f7c62c
  4. Rename tcga_cancer2filepath.json to tcga_index.json

    d278bf2
  5. Rename gtex_tissue2filepath.json to gtex_index.json

    c2f5f58
  6. Added .json files mapping study/tissue/cancer ids to sra/gtex/tcga filepaths in recount3-opendata bucket.

    ea5c6f0
  7. initial commit

    1b57ba5