Difference between revisions of "Resources"

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__NOTOC__
 
==Software==
 
==Software==
 
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*'''CTK''': CLIP Tool Kit, previously known as CIMS ([[CTK_Documentation|documentation]], [[CTK_Documentation#Download|download]], [https://groups.google.com/forum/#!forum/ctk-user-group user group])
 
*'''mCarts''': hidden Markov model (HMM) based methods to predict clusters RNA motif sites ([[mCarts_Documentation|documentation]], [[mCarts_Documentation#Download|download]])
 
*'''mCarts''': hidden Markov model (HMM) based methods to predict clusters RNA motif sites ([[mCarts_Documentation|documentation]], [[mCarts_Documentation#Download|download]])
*'''Qantas''': A pipeline to analyze alternative splicing using RNA-Seq ([[Quantas_Documentation|documentation]])
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*'''mCross''': modeling RBP binding specificity by registering protein-RNA crosslink sites ([[MCross|site]])
*'''OLego''': A tool for fast and accurate mapping of exon-junction reads ([[OLego_Documentation|documentation]], [[OLego_Documentation#Download|download]])
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*'''mRIN''': direct assessment of mRNA integrity from RNA-Seq data ([[mRIN|documentation]])
 
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*'''NDDcluster''': nonparametric "shape free" clustering algorithm based on normalized density derivatives ([[NDDcluster|site]])
==Database==
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*'''OLego''': A tool for fast and accurate mapping of exon-junction reads ([[OLego|site]], [[OLego_Documentation|documentation]], [[OLego_Documentation#Download|download]])
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*'''Splicescope''': prediction of neuronal maturation stages using splicing profile ([[Splicescope|site]])
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*'''Quantas''': A pipeline to analyze alternative splicing using RNA-Seq ([[Quantas_Documentation|documentation]],[[Quantas_Documentation#Download|download]])
  
*'''Splicebase''': a database of alternative splicing and regulation
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==Datasets==
  
==Protocols==
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*[[Cortex AS]]: Cortex_AS|A database of known and novel AS events in the brain
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*[[Autism_D-score|Autism D-score]]: Prioritization of autism risk genes using D-score derived from CSN cell type-specific gene expression.

Revision as of 10:24, 24 June 2019

Software

  • CTK: CLIP Tool Kit, previously known as CIMS (documentation, download, user group)
  • 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)
  • Splicescope: prediction of neuronal maturation stages using splicing profile (site)
  • Quantas: A pipeline to analyze alternative splicing using RNA-Seq (documentation,download)

Datasets

  • 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.