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Resources
From Zhang Laboratory
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We are committed to making resources generated in the lab, including datasets and software tools, available for the research communities.
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Software
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- 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)
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Datasets
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- 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.
- mCross RBP motifs: PWMs of 112 RBPs from our mCross paper, also see the web interface
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Reagents
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