Difference between revisions of "Resources"

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[[File:Resources.png|860px|center|link=]]
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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==
 
==Software==
  
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*'''CIMS''': Crosslinking induced mutation site (CIMS) analysis. It also includes some other tools for CLIP data analysis ([[CIMS_Documentation|documentation]], [[CIMS_Documentation#Download|download]])
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**scripts for cross linking induced truncation site (CITS) analysis are now included.
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[[File:Software2.png|80px|center|link=]]
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*'''CTK''': CLIP Tool Kit, previously known as CIMS ([[CTK_Documentation|documentation]], [[CTK_Documentation#Download|download]], [http://groups.google.com/forum/#!forum/ctk-user-group user group])
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*'''DeltaSplice''': deep neural network based prediction of alternative splicing and splicing-altering mutations from pre-mRNA sequences ([http://github.com/chaolinzhanglab/DeltaSplice site])
 
*'''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]])
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*'''mCross''': modeling RBP binding specificity by registering protein-RNA crosslink sites ([[MCross|site]])
 
*'''mRIN''': direct assessment of mRNA integrity from RNA-Seq data ([[mRIN|documentation]])
 
*'''mRIN''': direct assessment of mRNA integrity from RNA-Seq data ([[mRIN|documentation]])
 
*'''NDDcluster''': nonparametric "shape free" clustering algorithm based on normalized density derivatives ([[NDDcluster|site]])
 
*'''NDDcluster''': nonparametric "shape free" clustering algorithm based on normalized density derivatives ([[NDDcluster|site]])
 
*'''OLego''': A tool for fast and accurate mapping of exon-junction reads ([[OLego|site]], [[OLego_Documentation|documentation]], [[OLego_Documentation#Download|download]])
 
*'''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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*'''PxR3D-map''': structure-based prediction of protein-RNA photocrosslink sites ([http://github.com/chaolinzhanglab/PxR3D site])
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*'''Splicescope''': prediction of neuronal maturation stages using splicing profile ([[Splicescope|site]])
 
*'''Quantas''': A pipeline to analyze alternative splicing using RNA-Seq ([[Quantas_Documentation|documentation]],[[Quantas_Documentation#Download|download]])
 
*'''Quantas''': A pipeline to analyze alternative splicing using RNA-Seq ([[Quantas_Documentation|documentation]],[[Quantas_Documentation#Download|download]])
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==Datasets==
 
==Datasets==
  
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*Cortex AS: [[Cortex_AS|A database of known and novel AS events in the brain]]
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[[File:Datset.jpg|60px|center|link=]]
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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.
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*[http://zhanglab.c2b2.columbia.edu/data/mCross/eCLIP_mCross_PWM.tgz mCross RBP motifs]: PWMs of 112 RBPs from our mCross paper, also see the [http://zhanglab.c2b2.columbia.edu/mCrossBase/ web interface]
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==Reagents==
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[[File:Experiments.jpg|120px|center|link=]]
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*Plasmids: [http://www.addgene.org/Chaolin_Zhang/ available at Addgene]
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Latest revision as of 09:02, 30 May 2024


Resources.png

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



Software

Software2.png
  • 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)

Datasets

Datset.jpg
  • 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

Reagents

Experiments.jpg
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