Shen Lab

Public Tools

  • MAGPIE Webserver

    Multimodal Analysis Generated Pathogenic Impact Evaluator

  • SpTransformer Webserver

    The SpliceTransformer (SpTransformer) is a deep learning tool designed to predict tissue-specific splicing sites from pre-mRNA sequences.

  • Anchored-fusion Github repository

    The Anchored-fusion is a bioinformatic tool which detects fusion genes bases on paired-end RNA-sequence with ultrahigh sensitivity. Anchored-fusion target on the gene you choose, it will give the fusion genes including the target gene. Other fusion genes will not be represented in the output file.

  • RESA Github repository

    RESA detects somatic mutation with high precision directly from scRNA-seq data. The key assumption of this method is that cancer cells evolve in a clonal manner and thus expressed somatic mutations have cross-cell recurrence, whereas the noise and artefacts are likely distributed randomly with small probability of recurrence across the cell population. RESA is composed of three main steps: initial variant calling, filtering and labeling, and modeling and refinement.