From Zhang Laboratory

Jump to: navigation, search


We are committed to making resources generated in the lab, including datasets and software tools, available for the research communities.


  • CTK: CLIP Tool Kit, previously known as CIMS (documentation, download, user group)
  • DeltaSplice: deep neural network based prediction of alternative splicing and splicing-altering mutations from pre-mRNA sequences (site)
  • mCarts: hidden Markov model (HMM) based methods to predict clusters RNA motif sites (documentation, download)
  • mCross: modeling RBP binding specificity by registering protein-RNA crosslink sites (site)
  • mRIN: direct assessment of mRNA integrity from RNA-Seq data (documentation)
  • NDDcluster: nonparametric "shape free" clustering algorithm based on normalized density derivatives (site)
  • OLego: A tool for fast and accurate mapping of exon-junction reads (site, documentation, download)
  • PxR3D-map: structure-based prediction of protein-RNA photocrosslink sites (site)
  • Splicescope: prediction of neuronal maturation stages using splicing profile (site)
  • Quantas: A pipeline to analyze alternative splicing using RNA-Seq (documentation,download)


  • Cortex AS: Cortex_AS|A database of known and novel AS events in the brain
  • Autism D-score: Prioritization of autism risk genes using D-score derived from CSN cell type-specific gene expression.