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Example input files for isopret

RNA-Seq datasets were obtained from NCBI's Sequence Read Archive (SRA). These experiments study a broad range of conditons, but they all contained two distinct sets of samples that could be compared in a case-control design.

A zip archive containing HBADEALS output files for each of the datasets can be obtained from the zenodo archive at 10369086.

Details and PubMed identifiers for each of the experiments are available in the Supplementary material.

  • Supplemental table S1: 33 disease-related cohorts
  • Supplemental table S2: 28 RNA-seq experiments devoted primarily to the study of physiology, gene expression or cell biology.
  • Supplemental table S3: 39 RNA-seq experiments devoted primarily to the study of cancer
  • Supplemental table S4: 5 RNA-seq experiments related to infectious disease.

Additionally, the GitHub repository for the paper Betacoronavirus-specific alternate splicing also contains 15 HBA-DEALS output files related to that publication that can be used as input for isopretGO.